From 6e61e0fc10b0e0f76d75ef686e5214dfb5a6f8db Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Mon, 20 Nov 2017 15:11:55 +0400
Subject: [PATCH 01/45] lets see if it works with cache

---
 recipes/gencore_rnaseq/1.0/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index 945b6a1..a14484a 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -1,6 +1,7 @@
 {% set name = "gencore_rnaseq" %}
 {% set version = "1.0" %}
 
+
 package:
   name: {{ name }}
   version: {{ version }}

From 70bfbe18436849ae7dab122f8baea647f07cc75c Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Tue, 21 Nov 2017 10:10:32 +0400
Subject: [PATCH 02/45] commit

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 01967bc..5796c51 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -8,7 +8,7 @@ cache:
   - "/home/travis/.conda/pkgs"
 jobs:
   include:
-  - stage: Linux+macOS
+  - stage: Linux
     if: "(type = push) AND ((branch IN (master, bulk)) OR (fork = true))"
     os: linux
     script: scripts/travis-run.sh

From cbc2661ad84ad8379764ebf6aa51d9fbde4b33ba Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Tue, 5 Dec 2017 13:52:41 +0400
Subject: [PATCH 03/45] rnaseq

---
 configs/bioconda_utils-requirements.txt | 23 +++++++++++++++++++++++
 recipes/gencore_rnaseq/1.0/meta.yaml    |  1 +
 scripts/travis-run.sh                   |  3 +--
 scripts/travis-setup.sh                 |  6 ++----
 4 files changed, 27 insertions(+), 6 deletions(-)
 create mode 100644 configs/bioconda_utils-requirements.txt

diff --git a/configs/bioconda_utils-requirements.txt b/configs/bioconda_utils-requirements.txt
new file mode 100644
index 0000000..4feb63d
--- /dev/null
+++ b/configs/bioconda_utils-requirements.txt
@@ -0,0 +1,23 @@
+anaconda-client=1.6.3
+argh=0.26.2
+beautifulsoup4=4.6.0
+conda=4.3.21
+conda-build=2.1.16
+galaxy-lib=17.9.7
+jinja2=2.9.6
+jsonschema=2.5.1
+networkx=1.11
+pyaml=15.8.2
+pydotplus=2.0.2
+python=3.5.2
+requests=2.12.4
+sphinx
+docutils
+sphinx_rtd_theme
+involucro=1.1.2
+pandas=0.19.2
+numpy=1.12.1
+pygithub=1.29
+colorlog=2.10.*
+six=1.10.0
+alabaster=0.7.9
diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index a14484a..99e282b 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -53,3 +53,4 @@ about:
   home: 'https://cgsb.abudhabi.nyu.edu/'
   license: BSD
   summary: 'Gencore RnaSeq Module'
+
diff --git a/scripts/travis-run.sh b/scripts/travis-run.sh
index 11e818c..1e9fdd5 100755
--- a/scripts/travis-run.sh
+++ b/scripts/travis-run.sh
@@ -8,7 +8,6 @@ set +u
 [[ -z $RANGE_ARG ]] && RANGE_ARG="--git-range master HEAD"
 [[ -z $DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK  ]] && DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK="false"
 [[ -z $SKIP_LINTING ]] && SKIP_LINTING=false
-# [[ -z $CONTAINER_NAMESPACE ]] && CONTAINER_NAMESPACE="nyuad_cgsb"
 set -u
 
 if [[ $TRAVIS_BRANCH != "master" && $TRAVIS_BRANCH != "bulk" && $TRAVIS_PULL_REQUEST == "false" && $TRAVIS_REPO_SLUG == "$MY_TRAVIS_REPO_SLUG" ]]
@@ -111,6 +110,6 @@ fi
 
 set -x
 pip install --upgrade  git+https://github.com/jerowe/bioconda-utils.git@develop
-bioconda-utils build recipes config.yml $UPLOAD_ARG $DOCKER_ARG $BIOCONDA_UTILS_BUILD_ARGS $RANGE_ARG || echo "Build Failed!"
+bioconda-utils build recipes config.yml --channels nyuad-cgsb $UPLOAD_ARG $DOCKER_ARG $BIOCONDA_UTILS_BUILD_ARGS $RANGE_ARG || echo "Build Failed!"
 docker images
 set +x
diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh
index 77b7d03..24a8919 100755
--- a/scripts/travis-setup.sh
+++ b/scripts/travis-setup.sh
@@ -29,7 +29,5 @@ sudo chown -R $USER /anaconda
 $SCRIPT_DIR/../simulate-travis.py --bootstrap /anaconda --overwrite
 /anaconda/bin/conda index /anaconda/conda-bld/linux-64 /anaconda/conda-bld/osx-64
 /anaconda/bin/conda config --add channels file://anaconda/conda-bld
-/anaconda/bin/conda install -y r-base r-essentials openjdk perl bioconductor-biobase
-
-/anaconda/bin/conda info
-ls -lah /home/travis/.conda/pkgs
+/anaconda/bin/conda install -y r-base r-essentials openjdk perl bioconductor-biobase nodejs
+/anaconda/bin/npm install marked-man 

From 65c6e513d8d20b9b56cd3ecfda8f755dbc939bbc Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Tue, 5 Dec 2017 14:13:24 +0400
Subject: [PATCH 04/45] build rnaseq

---
 recipes/gencore_rnaseq/1.0/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index 99e282b..4097260 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -54,3 +54,4 @@ about:
   license: BSD
   summary: 'Gencore RnaSeq Module'
 
+

From acab09a2fb8c3ec00690152f94b1831c1fc5eb26 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Tue, 5 Dec 2017 14:21:20 +0400
Subject: [PATCH 05/45] commit

---
 scripts/travis-run.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/travis-run.sh b/scripts/travis-run.sh
index 1e9fdd5..029fc1c 100755
--- a/scripts/travis-run.sh
+++ b/scripts/travis-run.sh
@@ -110,6 +110,6 @@ fi
 
 set -x
 pip install --upgrade  git+https://github.com/jerowe/bioconda-utils.git@develop
-bioconda-utils build recipes config.yml --channels nyuad-cgsb $UPLOAD_ARG $DOCKER_ARG $BIOCONDA_UTILS_BUILD_ARGS $RANGE_ARG || echo "Build Failed!"
+bioconda-utils build recipes config.yml --channel nyuad-cgsb $UPLOAD_ARG $DOCKER_ARG $BIOCONDA_UTILS_BUILD_ARGS $RANGE_ARG || echo "Build Failed!"
 docker images
 set +x

From 1e3503a54722e8f8c7112e480a955d9a9c482db8 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Tue, 5 Dec 2017 14:21:43 +0400
Subject: [PATCH 06/45] rnaseq

---
 recipes/gencore_rnaseq/1.0/meta.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index 4097260..99e282b 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -54,4 +54,3 @@ about:
   license: BSD
   summary: 'Gencore RnaSeq Module'
 
-

From 58b1676760d1f3398403844a8c360ba30d5826ed Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Tue, 5 Dec 2017 14:44:17 +0400
Subject: [PATCH 07/45] commiting

---
 recipes/gencore_rnaseq/1.0/meta.yaml | 1 +
 scripts/travis-run.sh                | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index 99e282b..4097260 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -54,3 +54,4 @@ about:
   license: BSD
   summary: 'Gencore RnaSeq Module'
 
+
diff --git a/scripts/travis-run.sh b/scripts/travis-run.sh
index 029fc1c..48804a8 100755
--- a/scripts/travis-run.sh
+++ b/scripts/travis-run.sh
@@ -110,6 +110,6 @@ fi
 
 set -x
 pip install --upgrade  git+https://github.com/jerowe/bioconda-utils.git@develop
-bioconda-utils build recipes config.yml --channel nyuad-cgsb $UPLOAD_ARG $DOCKER_ARG $BIOCONDA_UTILS_BUILD_ARGS $RANGE_ARG || echo "Build Failed!"
+bioconda-utils build recipes config.yml  $UPLOAD_ARG $DOCKER_ARG $BIOCONDA_UTILS_BUILD_ARGS $RANGE_ARG || echo "Build Failed!"
 docker images
 set +x

From 838af343b544a7701a83f859c648a0bcfb22a2bf Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Thu, 7 Dec 2017 11:01:30 +0400
Subject: [PATCH 08/45] starting new branch stupid rnaseq

---
 .gitignore                                    |  1 +
 recipes/gencore_rnaseq/1.0/meta.yaml          | 32 +++++++++----------
 .../gencore_rnaseq_alignment/1.0/meta.yaml    | 30 +++++++++++++++++
 3 files changed, 46 insertions(+), 17 deletions(-)
 create mode 100644 .gitignore
 create mode 100644 recipes/gencore_rnaseq_alignment/1.0/meta.yaml

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..b237adb
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+set_envs.sh
diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index 4097260..db805f4 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -12,38 +12,38 @@ build:
 
 requirements:
   run:
+  ##Alignment
   - samtools ==1.3.1
-  - bcftools ==1.3.1
   - kallisto ==0.43.0
+  - cufflinks-patch ==2.2.1
+  - bowtie2 ==2.2.8
+  - tophat ==2.1.0
+  - star ==2.5.2a
+  - bcftools ==1.3.1
   - blat ==35
   - gatk ==3.6
   - picard ==2.5.0
-  - trimmomatic ==0.36
-  - fastqc ==0.11.5
   - prinseq ==0.20.4
-  - star ==2.5.2a
   - vcftools ==0.1.14
   - bedtools ==2.25.0
   - vcflib ==1.0.0_rc1
   - bamtools ==2.4.0
   - seqtk ==1.2
-  - bowtie2 ==2.2.8
-  - tophat ==2.1.0
-  - cufflinks-patch ==2.2.1
+  ##Downstream processing
   - r-base
   - r-essentials
   - r-cairo
   - bioconductor-deseq2
   - bioconductor-edger >=3.14.0
   - bioconductor-cummerbund >=2.16.0
-  - bioconductor-genomicranges >=1.26.1
-  - bioconductor-gviz >=1.16.5
-  - bioconductor-biovizbase >=1.18.0
-  - bioconductor-s4vectors >=0.12.0
-  - bioconductor-ballgown >=2.2.0
-  - htseq ==0.6.1.post1
-  - hisat2 ==2.0.4
-  - stringtie ==1.3.0
+  # - bioconductor-genomicranges >=1.26.1
+  # - bioconductor-gviz >=1.16.5
+  # - bioconductor-biovizbase >=1.18.0
+  # - bioconductor-s4vectors >=0.12.0
+  # - bioconductor-ballgown >=2.2.0
+  # - htseq ==0.6.1.post1
+  # - hisat2 ==2.0.4
+  # - stringtie ==1.3.0
 
 test:
   commands:
@@ -53,5 +53,3 @@ about:
   home: 'https://cgsb.abudhabi.nyu.edu/'
   license: BSD
   summary: 'Gencore RnaSeq Module'
-
-
diff --git a/recipes/gencore_rnaseq_alignment/1.0/meta.yaml b/recipes/gencore_rnaseq_alignment/1.0/meta.yaml
new file mode 100644
index 0000000..cc83403
--- /dev/null
+++ b/recipes/gencore_rnaseq_alignment/1.0/meta.yaml
@@ -0,0 +1,30 @@
+{% set name = "gencore_rnaseq_alignment" %}
+{% set version = "1.0" %}
+
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+build:
+  number: 0
+  skip: True # [osx]
+
+requirements:
+  run:
+  ##Alignment
+  - samtools ==1.3.1
+  - kallisto ==0.43.0
+  - cufflinks-patch ==2.2.1
+  - bowtie2 ==2.2.8
+  - tophat ==2.1.0
+  - star ==2.5.2a
+
+test:
+  commands:
+    - bowtie2 --help 2>&1 | grep 'bowtie'
+
+about:
+  home: 'https://cgsb.abudhabi.nyu.edu/'
+  license: BSD
+  summary: 'Gencore RnaSeq Module'

From 8fe3aff240a2141c19bda221536a890d23b3e631 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Fri, 8 Dec 2017 09:20:35 +0400
Subject: [PATCH 09/45] commit

---
 .gitignore                           | 1 +
 recipes/gencore_rnaseq/1.0/meta.yaml | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index b237adb..535b6dc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
 set_envs.sh
+involucro
diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index db805f4..71c1cd7 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -47,7 +47,7 @@ requirements:
 
 test:
   commands:
-    - bowtie2 --help 2>&1 | grep 'bowtie'
+    - bowtie2 --help 2>&1 | grep "bowtie"
 
 about:
   home: 'https://cgsb.abudhabi.nyu.edu/'

From 1a1713e598d1c6b21f021d17264bef31cbfcc33a Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Fri, 8 Dec 2017 09:43:39 +0400
Subject: [PATCH 10/45] trying ot see if this will speed up build

---
 scripts/travis-run.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/travis-run.sh b/scripts/travis-run.sh
index 48804a8..873bc14 100755
--- a/scripts/travis-run.sh
+++ b/scripts/travis-run.sh
@@ -73,7 +73,8 @@ export PATH=/anaconda/bin:$PATH
 # for local testing.
 if [[ $TRAVIS_OS_NAME == "linux" && $TRAVIS == "true" ]]
 then
-    DOCKER_ARG="--docker --mulled-test"
+    #DOCKER_ARG="--docker --mulled-test"
+    DOCKER_ARG=" --mulled-test"
 fi
 
 # When building master or bulk, upload packages to anaconda and quay.io.

From f218aca273b06ae5a8b934bcf431f8381acdd8b3 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Fri, 8 Dec 2017 09:59:25 +0400
Subject: [PATCH 11/45] try this

---
 scripts/travis-run.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/travis-run.sh b/scripts/travis-run.sh
index 873bc14..30afd8c 100755
--- a/scripts/travis-run.sh
+++ b/scripts/travis-run.sh
@@ -73,8 +73,8 @@ export PATH=/anaconda/bin:$PATH
 # for local testing.
 if [[ $TRAVIS_OS_NAME == "linux" && $TRAVIS == "true" ]]
 then
-    #DOCKER_ARG="--docker --mulled-test"
-    DOCKER_ARG=" --mulled-test"
+    DOCKER_ARG="--docker --mulled-test"
+    #DOCKER_ARG=" --mulled-test"
 fi
 
 # When building master or bulk, upload packages to anaconda and quay.io.

From c22263490c45e2751c952cf51aab453542a4073e Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Fri, 8 Dec 2017 10:05:54 +0400
Subject: [PATCH 12/45] building cache dir

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 5796c51..0a72eef 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,7 +5,7 @@ services:
 install: scripts/travis-setup.sh
 cache:
   directories:
-  - "/home/travis/.conda/pkgs"
+  - "/anaconda/conda-bld/pkg-cache"
 jobs:
   include:
   - stage: Linux
@@ -27,7 +27,7 @@ env:
   - GITHUB_USER='nyuad-cgsb'
   - MY_TRAVIS_REPO_SLUG='biosails/biostacks'
   - CONTAINER_NAMESPACE='nyuad_cgsb'
-  - CONDA_PKGS_DIRS='/home/travis/.conda/pkgs'
+  - CONDA_PKGS_DIRS='/anaconda/conda-bld/pkg-cache'
   - secure: 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
   - secure: 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
   - secure: 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

From e6a539b78b8fc04ef4af39737c4b00788cb64a9b Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Fri, 8 Dec 2017 10:23:40 +0400
Subject: [PATCH 13/45] trying ot add in package cache

---
 .travis.yml             | 4 ++--
 scripts/travis-setup.sh | 4 +++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 0a72eef..4f11641 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,7 +5,7 @@ services:
 install: scripts/travis-setup.sh
 cache:
   directories:
-  - "/anaconda/conda-bld/pkg-cache"
+  - "/opt/anaconda-pkg-cache"
 jobs:
   include:
   - stage: Linux
@@ -27,7 +27,7 @@ env:
   - GITHUB_USER='nyuad-cgsb'
   - MY_TRAVIS_REPO_SLUG='biosails/biostacks'
   - CONTAINER_NAMESPACE='nyuad_cgsb'
-  - CONDA_PKGS_DIRS='/anaconda/conda-bld/pkg-cache'
+  - CONDA_PKGS_DIRS='/opt/anaconda-pkg-cache'
   - secure: 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
   - secure: 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
   - secure: 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
diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh
index 24a8919..16b71f7 100755
--- a/scripts/travis-setup.sh
+++ b/scripts/travis-setup.sh
@@ -25,9 +25,11 @@ SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 
 pip install pyyaml
 sudo mkdir /anaconda
+sudo mkdir -p /opt/anaconda-pkg-cache
+sudo chown -R $USER /opt/anaconda-pkg-cache
 sudo chown -R $USER /anaconda
 $SCRIPT_DIR/../simulate-travis.py --bootstrap /anaconda --overwrite
 /anaconda/bin/conda index /anaconda/conda-bld/linux-64 /anaconda/conda-bld/osx-64
 /anaconda/bin/conda config --add channels file://anaconda/conda-bld
 /anaconda/bin/conda install -y r-base r-essentials openjdk perl bioconductor-biobase nodejs
-/anaconda/bin/npm install marked-man 
+/anaconda/bin/npm install marked-man

From 8b49298eaa513148683199985c669c26213ea021 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Sat, 9 Dec 2017 11:38:35 +0400
Subject: [PATCH 14/45] try this

---
 recipes/gencore_rnaseq/1.0/meta.yaml | 1 -
 recipes/gencore_test/1.0/meta.yaml   | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index f102083..da71699 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -1,7 +1,6 @@
 {% set name = "gencore_rnaseq" %}
 {% set version = "1.0" %}
 
-
 package:
   name: {{ name }}
   version: {{ version }}
diff --git a/recipes/gencore_test/1.0/meta.yaml b/recipes/gencore_test/1.0/meta.yaml
index 530a4e1..e9eebab 100644
--- a/recipes/gencore_test/1.0/meta.yaml
+++ b/recipes/gencore_test/1.0/meta.yaml
@@ -13,6 +13,7 @@ build:
 requirements:
   run:
     - perl
+    - cufflinks-patch
 
 test:
   commands:

From ac698e7a0bb3b12c16c4c26bcd81b2f159850434 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Sat, 9 Dec 2017 11:39:29 +0400
Subject: [PATCH 15/45] commit

---
 recipes/gencore_rnaseq/1.0/meta.yaml          |  1 +
 .../gencore_rnaseq_alignment/1.0/meta.yaml    | 30 -------------------
 2 files changed, 1 insertion(+), 30 deletions(-)
 delete mode 100644 recipes/gencore_rnaseq_alignment/1.0/meta.yaml

diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index da71699..f102083 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -1,6 +1,7 @@
 {% set name = "gencore_rnaseq" %}
 {% set version = "1.0" %}
 
+
 package:
   name: {{ name }}
   version: {{ version }}
diff --git a/recipes/gencore_rnaseq_alignment/1.0/meta.yaml b/recipes/gencore_rnaseq_alignment/1.0/meta.yaml
deleted file mode 100644
index cc83403..0000000
--- a/recipes/gencore_rnaseq_alignment/1.0/meta.yaml
+++ /dev/null
@@ -1,30 +0,0 @@
-{% set name = "gencore_rnaseq_alignment" %}
-{% set version = "1.0" %}
-
-
-package:
-  name: {{ name }}
-  version: {{ version }}
-
-build:
-  number: 0
-  skip: True # [osx]
-
-requirements:
-  run:
-  ##Alignment
-  - samtools ==1.3.1
-  - kallisto ==0.43.0
-  - cufflinks-patch ==2.2.1
-  - bowtie2 ==2.2.8
-  - tophat ==2.1.0
-  - star ==2.5.2a
-
-test:
-  commands:
-    - bowtie2 --help 2>&1 | grep 'bowtie'
-
-about:
-  home: 'https://cgsb.abudhabi.nyu.edu/'
-  license: BSD
-  summary: 'Gencore RnaSeq Module'

From ad5725b59bd902d0ce45d099fd4d30e3c5ab4b36 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Sun, 10 Dec 2017 06:00:20 +0400
Subject: [PATCH 16/45] BUILD

---
 recipes/gencore_rnaseq/1.0/meta.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index f102083..da71699 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -1,7 +1,6 @@
 {% set name = "gencore_rnaseq" %}
 {% set version = "1.0" %}
 
-
 package:
   name: {{ name }}
   version: {{ version }}

From 644dc4605e3d2bbd84315041be7b331751b94b9f Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Sun, 10 Dec 2017 06:10:20 +0400
Subject: [PATCH 17/45] commiting

---
 recipes/gencore_rnaseq/1.0/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index da71699..f102083 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -1,6 +1,7 @@
 {% set name = "gencore_rnaseq" %}
 {% set version = "1.0" %}
 
+
 package:
   name: {{ name }}
   version: {{ version }}

From e5627a3b14480ca8f4056c806cbe7e741efc9839 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Sun, 10 Dec 2017 09:50:23 +0400
Subject: [PATCH 18/45] lets try this

---
 recipes/gencore_rnaseq/1.0/meta.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index f102083..7082cdf 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -1,13 +1,12 @@
 {% set name = "gencore_rnaseq" %}
 {% set version = "1.0" %}
 
-
 package:
   name: {{ name }}
   version: {{ version }}
 
 build:
-  number: 0
+  number: 1
   skip: True # [osx]
 
 requirements:

From 2cc941d75ec13dd79631385200ee9c538b15b375 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Mon, 11 Dec 2017 09:43:23 +0400
Subject: [PATCH 19/45] reopen

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index 4f11641..c640be1 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -35,3 +35,4 @@ env:
   - SUBDAG=0
 matrix:
   fast_finish: true
+

From 0434f79689223ce2e5ba85f27b68e6ee66648d3f Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Mon, 11 Dec 2017 10:00:26 +0400
Subject: [PATCH 20/45] incremental build

---
 recipes/gencore_rnaseq/1.0/meta.yaml | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index 7082cdf..711d7dc 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -29,20 +29,20 @@ requirements:
   - bamtools ==2.4.0
   - seqtk ==1.2
   ##Downstream processing
-  - r-base
-  - r-essentials
-  - r-cairo
-  - bioconductor-deseq2
-  - bioconductor-edger >=3.14.0
-  - bioconductor-cummerbund >=2.16.0
-  - bioconductor-genomicranges >=1.26.1
-  - bioconductor-gviz >=1.16.5
-  - bioconductor-biovizbase >=1.18.0
-  - bioconductor-s4vectors >=0.12.0
-  - bioconductor-ballgown >=2.2.0
-  - htseq ==0.6.1.post1
-  - hisat2 ==2.0.4
-  - stringtie ==1.3.0
+  # - r-base
+  # - r-essentials
+  # - r-cairo
+  # - bioconductor-deseq2
+  # - bioconductor-edger >=3.14.0
+  # - bioconductor-cummerbund >=2.16.0
+  # - bioconductor-genomicranges >=1.26.1
+  # - bioconductor-gviz >=1.16.5
+  # - bioconductor-biovizbase >=1.18.0
+  # - bioconductor-s4vectors >=0.12.0
+  # - bioconductor-ballgown >=2.2.0
+  # - htseq ==0.6.1.post1
+  # - hisat2 ==2.0.4
+  # - stringtie ==1.3.0
 
 test:
   commands:

From fef85cec2e39c853534374dfecc4756df7fcb031 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Mon, 11 Dec 2017 10:22:16 +0400
Subject: [PATCH 21/45] commit

---
 .travis.yml                          | 3 +--
 recipes/gencore_rnaseq/1.0/meta.yaml | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index c640be1..b144728 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -20,7 +20,7 @@ env:
   global:
   - SUBDAGS=1
   - BIOCONDA_UTILS_TAG=master
-  - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=info"
+  - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=debug"
   - BIOCONDA_UTILS_LINT_ARGS=
   - MINICONDA_VER="4.3.21"
   - ANACONDA_USER='nyuad-cgsb'
@@ -35,4 +35,3 @@ env:
   - SUBDAG=0
 matrix:
   fast_finish: true
-
diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index 711d7dc..83f5444 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -29,7 +29,7 @@ requirements:
   - bamtools ==2.4.0
   - seqtk ==1.2
   ##Downstream processing
-  # - r-base
+  - r-base
   # - r-essentials
   # - r-cairo
   # - bioconductor-deseq2

From c8266b603221a06b6ba5b6edad965185634d804c Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Mon, 11 Dec 2017 11:22:47 +0400
Subject: [PATCH 22/45] try it without the docker

---
 scripts/travis-run.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/travis-run.sh b/scripts/travis-run.sh
index 30afd8c..cb297e4 100755
--- a/scripts/travis-run.sh
+++ b/scripts/travis-run.sh
@@ -73,7 +73,7 @@ export PATH=/anaconda/bin:$PATH
 # for local testing.
 if [[ $TRAVIS_OS_NAME == "linux" && $TRAVIS == "true" ]]
 then
-    DOCKER_ARG="--docker --mulled-test"
+    DOCKER_ARG="--mulled-test"
     #DOCKER_ARG=" --mulled-test"
 fi
 

From 044b769db720a0fcc78a098fe723aac9bcf74212 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 09:20:30 +0400
Subject: [PATCH 23/45] BUILD

---
 .travis.yml                          |  5 +++--
 Dockerfile                           | 14 ++++++++++++++
 recipes/gencore_rnaseq/1.0/meta.yaml | 26 +++++++++++++-------------
 recipes/gencore_test/1.0/meta.yaml   |  1 -
 scripts/build_docs.py                | 11 +++++++++++
 scripts/travis-setup.sh              |  5 +++--
 6 files changed, 44 insertions(+), 18 deletions(-)
 create mode 100644 Dockerfile
 create mode 100644 scripts/build_docs.py

diff --git a/.travis.yml b/.travis.yml
index b144728..ef40ef9 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,7 +5,7 @@ services:
 install: scripts/travis-setup.sh
 cache:
   directories:
-  - "/opt/anaconda-pkg-cache"
+  - "/opt/anaconda3/pkgs"
 jobs:
   include:
   - stage: Linux
@@ -27,7 +27,8 @@ env:
   - GITHUB_USER='nyuad-cgsb'
   - MY_TRAVIS_REPO_SLUG='biosails/biostacks'
   - CONTAINER_NAMESPACE='nyuad_cgsb'
-  - CONDA_PKGS_DIRS='/opt/anaconda-pkg-cache'
+  - CONDA_PKGS_DIRS='/opt/anaconda3/pkgs'
+  - CONDA_BLD_PATH='/opt/anaconda3/conda-bld'
   - secure: JHMiExNBJUTCd/cSXb7cY6DK4MmxIPO3IBfQAD6fSNOEXJe2KY9b8qAjxPwzKzD2FzQOZ1dln1rJiF/3HeVUEu3QN96PfhuqSeIaICP+m8q5ZHgQIyvHwDc09ne/yip1l6BIDtXCuNw/tYUZh3tgpw+bTve3cGXFiqYopvqMlZ2NcW/thQbpWCsdTnJq1g+Sq6DO3oRZm3WGdfS2sh3mv6TErXhQJi8nqWoNyOl2S6JGHRNOHp5vA11D24cAyxY+f5ezhp6Z3QxWL2mnnEwnazEC1PgcE6nA443R2fQRnF5q+ze42g+lSE3FTelWgwY2Jq5hIZRcov2Wj9H+i5zFDmnf503YZ2YLQ52WXnkPtuYCCOi5Sl7/qALLnjyLYNGoBCTZaONeToNSBs/058teuDZCDSLoLFCLlKnpPf1/FnkpEE8cegedHjvCeo2ffehCCrXiAoelUeAOscq9f7GSGa0UrybQckAhIQpR/J1C+FrOaOoFUXhtpxFFwxT6l36Vnt8i0dW0BKve6WU+DeG84JC5NnoULVK40Rg/VgGaB0qq1rX7+TWPw2kGWGWuAUDy+d6jAa+q41VzXjErmgeh3ftCtqS4TLS8tGGuhXkFj3wn9Z7fHIC0r82OqAQNyzj07hNk0MM/btGlU//bquyTFq4gwT2+jS3t1UqENFvAOA0=
   - secure: 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
   - secure: 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
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..481239d
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,14 @@
+from continuumio/miniconda3
+
+COPY /home/jillian/.eb/software/Anaconda3/5.0.1/pkgs /anaconda-pkg-cache
+COPY /home/jillian/.eb/software/Anaconda3/5.0.1/conda-bld /anaconda-conda-bld
+
+ENV CONDA_PKGS_DIRS /anaconda/pkg-cache 
+ENV CONDA_BLD_PATH /anaconda-conda-bld 
+
+RUN conda add --channels file://anaconda-conda-bld
+RUN conda index /anaconda-conda-bld/linux-64 
+
+RUN cat ~/.condarc
+
+RUN conda install -y gencore_test
diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index 83f5444..7082cdf 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -30,19 +30,19 @@ requirements:
   - seqtk ==1.2
   ##Downstream processing
   - r-base
-  # - r-essentials
-  # - r-cairo
-  # - bioconductor-deseq2
-  # - bioconductor-edger >=3.14.0
-  # - bioconductor-cummerbund >=2.16.0
-  # - bioconductor-genomicranges >=1.26.1
-  # - bioconductor-gviz >=1.16.5
-  # - bioconductor-biovizbase >=1.18.0
-  # - bioconductor-s4vectors >=0.12.0
-  # - bioconductor-ballgown >=2.2.0
-  # - htseq ==0.6.1.post1
-  # - hisat2 ==2.0.4
-  # - stringtie ==1.3.0
+  - r-essentials
+  - r-cairo
+  - bioconductor-deseq2
+  - bioconductor-edger >=3.14.0
+  - bioconductor-cummerbund >=2.16.0
+  - bioconductor-genomicranges >=1.26.1
+  - bioconductor-gviz >=1.16.5
+  - bioconductor-biovizbase >=1.18.0
+  - bioconductor-s4vectors >=0.12.0
+  - bioconductor-ballgown >=2.2.0
+  - htseq ==0.6.1.post1
+  - hisat2 ==2.0.4
+  - stringtie ==1.3.0
 
 test:
   commands:
diff --git a/recipes/gencore_test/1.0/meta.yaml b/recipes/gencore_test/1.0/meta.yaml
index e9eebab..530a4e1 100644
--- a/recipes/gencore_test/1.0/meta.yaml
+++ b/recipes/gencore_test/1.0/meta.yaml
@@ -13,7 +13,6 @@ build:
 requirements:
   run:
     - perl
-    - cufflinks-patch
 
 test:
   commands:
diff --git a/scripts/build_docs.py b/scripts/build_docs.py
new file mode 100644
index 0000000..0db8ef2
--- /dev/null
+++ b/scripts/build_docs.py
@@ -0,0 +1,11 @@
+#!/usr/bin/env python
+
+from conda_build.config import Config
+from conda_build.metadata import MetaData
+from conda_build.render import render_recipe
+
+recipe_dir = 'recipes/gencore_rnaseq/1.0/meta.yaml'
+
+config =  Config(croot=recipe_dir, anaconda_upload=False, verbose=True,
+activate=False, debug=False, variant=None)
+metadata = render_recipe(recipe_dir, config=config)
diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh
index 16b71f7..c4b06a0 100755
--- a/scripts/travis-setup.sh
+++ b/scripts/travis-setup.sh
@@ -25,9 +25,10 @@ SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 
 pip install pyyaml
 sudo mkdir /anaconda
-sudo mkdir -p /opt/anaconda-pkg-cache
-sudo chown -R $USER /opt/anaconda-pkg-cache
+
+sudo chown -R $USER /opt/anaconda3
 sudo chown -R $USER /anaconda
+
 $SCRIPT_DIR/../simulate-travis.py --bootstrap /anaconda --overwrite
 /anaconda/bin/conda index /anaconda/conda-bld/linux-64 /anaconda/conda-bld/osx-64
 /anaconda/bin/conda config --add channels file://anaconda/conda-bld

From 90a6d5b4d456b0e6b202fb67be1fe224bf78bf48 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 09:42:53 +0400
Subject: [PATCH 24/45] trying with conda-build-all instead

---
 .travis.yml                           | 33 ++++++++++++--------
 Dockerfile                            | 15 ++-------
 recipes/gencore_rnaseq/1.0/meta.yaml  | 22 ++++++-------
 scripts/travis-run-conda-build-all.sh | 45 +++++++++++++++++++++++++++
 4 files changed, 79 insertions(+), 36 deletions(-)
 create mode 100644 scripts/travis-run-conda-build-all.sh

diff --git a/.travis.yml b/.travis.yml
index ef40ef9..186e566 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,24 +11,31 @@ jobs:
   - stage: Linux
     if: "(type = push) AND ((branch IN (master, bulk)) OR (fork = true))"
     os: linux
-    script: scripts/travis-run.sh
+    script: scripts/travis-run-conda-build-all.sh
   - stage: Linux
     if: type = pull_request
     os: linux
-    script: scripts/travis-run.sh
+    script: scripts/travis-run-conda-build-all.sh
 env:
   global:
-  - SUBDAGS=1
-  - BIOCONDA_UTILS_TAG=master
-  - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=debug"
-  - BIOCONDA_UTILS_LINT_ARGS=
-  - MINICONDA_VER="4.3.21"
-  - ANACONDA_USER='nyuad-cgsb'
-  - GITHUB_USER='nyuad-cgsb'
-  - MY_TRAVIS_REPO_SLUG='biosails/biostacks'
-  - CONTAINER_NAMESPACE='nyuad_cgsb'
-  - CONDA_PKGS_DIRS='/opt/anaconda3/pkgs'
-  - CONDA_BLD_PATH='/opt/anaconda3/conda-bld'
+  - MINICONDA_VER: '4.3.21'
+  - ANACONDA_USER: 'nyuad-cgsb'
+  - GITHUB_USER: 'nyuad-cgsb'
+  - MY_TRAVIS_REPO_SLUG: 'biosails/biostacks'
+  - CONTAINER_NAMESPACE: 'nyuad_cgsb'
+  - CONDA_PKGS_DIRS: '/opt/anaconda3/pkgs'
+  - CONDA_BLD_PATH: '/opt/anaconda3/conda-bld'
+  # - SUBDAGS=1
+  # - BIOCONDA_UTILS_TAG=master
+  # - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=debug"
+  # - BIOCONDA_UTILS_LINT_ARGS=
+  # - MINICONDA_VER="4.3.21"
+  # - ANACONDA_USER='nyuad-cgsb'
+  # - GITHUB_USER='nyuad-cgsb'
+  # - MY_TRAVIS_REPO_SLUG='biosails/biostacks'
+  # - CONTAINER_NAMESPACE='nyuad_cgsb'
+  # - CONDA_PKGS_DIRS='/opt/anaconda3/pkgs'
+  # - CONDA_BLD_PATH='/opt/anaconda3/conda-bld'
   - secure: 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
   - secure: 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
   - secure: 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
diff --git a/Dockerfile b/Dockerfile
index 481239d..dc41f92 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,14 +1,5 @@
 from continuumio/miniconda3
 
-COPY /home/jillian/.eb/software/Anaconda3/5.0.1/pkgs /anaconda-pkg-cache
-COPY /home/jillian/.eb/software/Anaconda3/5.0.1/conda-bld /anaconda-conda-bld
-
-ENV CONDA_PKGS_DIRS /anaconda/pkg-cache 
-ENV CONDA_BLD_PATH /anaconda-conda-bld 
-
-RUN conda add --channels file://anaconda-conda-bld
-RUN conda index /anaconda-conda-bld/linux-64 
-
-RUN cat ~/.condarc
-
-RUN conda install -y gencore_test
+ARG CONDA_PKG=local
+ENV CONDA_PKG ${CONDA_PKG}
+RUN echo ${CONDA_PKG}
diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index 7082cdf..0323b20 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -32,17 +32,17 @@ requirements:
   - r-base
   - r-essentials
   - r-cairo
-  - bioconductor-deseq2
-  - bioconductor-edger >=3.14.0
-  - bioconductor-cummerbund >=2.16.0
-  - bioconductor-genomicranges >=1.26.1
-  - bioconductor-gviz >=1.16.5
-  - bioconductor-biovizbase >=1.18.0
-  - bioconductor-s4vectors >=0.12.0
-  - bioconductor-ballgown >=2.2.0
-  - htseq ==0.6.1.post1
-  - hisat2 ==2.0.4
-  - stringtie ==1.3.0
+  # - bioconductor-deseq2
+  # - bioconductor-edger >=3.14.0
+  # - bioconductor-cummerbund >=2.16.0
+  # - bioconductor-genomicranges >=1.26.1
+  # - bioconductor-gviz >=1.16.5
+  # - bioconductor-biovizbase >=1.18.0
+  # - bioconductor-s4vectors >=0.12.0
+  # - bioconductor-ballgown >=2.2.0
+  # - htseq ==0.6.1.post1
+  # - hisat2 ==2.0.4
+  # - stringtie ==1.3.0
 
 test:
   commands:
diff --git a/scripts/travis-run-conda-build-all.sh b/scripts/travis-run-conda-build-all.sh
new file mode 100644
index 0000000..0852c44
--- /dev/null
+++ b/scripts/travis-run-conda-build-all.sh
@@ -0,0 +1,45 @@
+#!/bin/bash
+set -euo pipefail
+# Set some defaults
+set +u
+[[ -z $DOCKER_ARG ]] && DOCKER_ARG=""
+[[ -z $TRAVIS ]] && TRAVIS="false"
+[[ -z $BIOCONDA_UTILS_LINT_ARGS ]] && BIOCONDA_UTILS_LINT_ARGS=""
+[[ -z $RANGE_ARG ]] && RANGE_ARG="--git-range master HEAD"
+[[ -z $DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK  ]] && DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK="false"
+[[ -z $SKIP_LINTING ]] && SKIP_LINTING=false
+set -u
+
+if [[ $TRAVIS_BRANCH != "master" && $TRAVIS_BRANCH != "bulk" && $TRAVIS_PULL_REQUEST == "false" && $TRAVIS_REPO_SLUG == "$MY_TRAVIS_REPO_SLUG" ]]
+then
+    echo ""
+    echo "Tests are skipped for pushes to the main bioconda-recipes repo."
+    echo "If you have opened a pull request, please see the full tests for that PR."
+    echo "See https://bioconda.github.io/build-system.html for details"
+    echo ""
+    exit 0
+fi
+
+export PATH=/anaconda/bin:$PATH
+
+# TODO Add another upload
+if [[ ( $TRAVIS_BRANCH == "master" || $TRAVIS_BRANCH == "bulk" ) && "$TRAVIS_PULL_REQUEST" == "false" && $TRAVIS_REPO_SLUG == "$MY_TRAVIS_REPO_SLUG" ]]
+then
+        UPLOAD_ARG="--upload-channels nyuad-cgsb "
+fi
+
+
+if [[ $DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK == "true" ]]
+then
+    echo
+    echo "DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK is true."
+    echo "A comprehensive check will be performed to see what needs to be built."
+    RANGE_ARG=""
+fi
+
+set -x
+conda-build-all recipes --inspect-channels nyuad-cgsb $UPLOAD_ARG
+ls -lahR $CONDA_BLD_PATH
+
+docker images
+set +x

From 07eff50702ae07f7b4fe7d7c22197aa690008518 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 09:46:18 +0400
Subject: [PATCH 25/45] trying build with conda-build-all instead

---
 scripts/travis-run-conda-build-all.sh |  1 +
 scripts/travis-setup.sh               | 12 ++++++++++--
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/scripts/travis-run-conda-build-all.sh b/scripts/travis-run-conda-build-all.sh
index 0852c44..c1282a6 100644
--- a/scripts/travis-run-conda-build-all.sh
+++ b/scripts/travis-run-conda-build-all.sh
@@ -38,6 +38,7 @@ then
 fi
 
 set -x
+conda install -y conda-build-all
 conda-build-all recipes --inspect-channels nyuad-cgsb $UPLOAD_ARG
 ls -lahR $CONDA_BLD_PATH
 
diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh
index c4b06a0..28b1bfa 100755
--- a/scripts/travis-setup.sh
+++ b/scripts/travis-setup.sh
@@ -29,8 +29,16 @@ sudo mkdir /anaconda
 sudo chown -R $USER /opt/anaconda3
 sudo chown -R $USER /anaconda
 
-$SCRIPT_DIR/../simulate-travis.py --bootstrap /anaconda --overwrite
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+bash miniconda.sh -b -p /anaconda3
+export PATH="/anaconda3/bin:$PATH"
+hash -r
+conda config --set always_yes yes --set changeps1 no
+conda config --add channels r
+conda config --add channels conda-forge
+conda config --add channels bioconda
+
 /anaconda/bin/conda index /anaconda/conda-bld/linux-64 /anaconda/conda-bld/osx-64
 /anaconda/bin/conda config --add channels file://anaconda/conda-bld
 /anaconda/bin/conda install -y r-base r-essentials openjdk perl bioconductor-biobase nodejs
-/anaconda/bin/npm install marked-man
+/anaconda/bin/npm install -g marked-man

From 113d6ccf454fbb990a0f22f34db996d20ea687a0 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 09:57:47 +0400
Subject: [PATCH 26/45] lets see if this works

---
 Dockerfile                            | 16 ++++++++++++++++
 scripts/travis-run-conda-build-all.sh |  3 +++
 2 files changed, 19 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index dc41f92..759f5a2 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,4 +2,20 @@ from continuumio/miniconda3
 
 ARG CONDA_PKG=local
 ENV CONDA_PKG ${CONDA_PKG}
+
 RUN echo ${CONDA_PKG}
+RUN which conda
+RUN conda info
+
+
+## We have to add the pkgs and the build-system
+COPY pkgs/* /opt/conda/pkgs/
+COPY conda-bld /opt/conda/conda-bld
+
+#RUN conda config --set always_yes yes --set changeps1 no
+#RUN conda config --add channels r
+#RUN conda config --add channels conda-forge
+#RUN conda config --add channels bioconda
+#RUN conda config --add channels nyuad-cgsb
+#
+# conda config --add channels file://anaconda-conda-bld/linux-64
diff --git a/scripts/travis-run-conda-build-all.sh b/scripts/travis-run-conda-build-all.sh
index c1282a6..69be0a5 100644
--- a/scripts/travis-run-conda-build-all.sh
+++ b/scripts/travis-run-conda-build-all.sh
@@ -42,5 +42,8 @@ conda install -y conda-build-all
 conda-build-all recipes --inspect-channels nyuad-cgsb $UPLOAD_ARG
 ls -lahR $CONDA_BLD_PATH
 
+cp Dockerfile /opt/anaconda3
+cd /opt/anaconda3
+
 docker images
 set +x

From ac79e2435ab5ac41cb59a613fa3e0f282bfc64c2 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 10:00:20 +0400
Subject: [PATCH 27/45] lets try the whole workflow

---
 Dockerfile                            | 6 +++---
 scripts/travis-run-conda-build-all.sh | 1 +
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 759f5a2..c13d24b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -6,11 +6,11 @@ ENV CONDA_PKG ${CONDA_PKG}
 RUN echo ${CONDA_PKG}
 RUN which conda
 RUN conda info
-
+RUN mkdir -p /opt/conda/conda-bld/linux-64
 
 ## We have to add the pkgs and the build-system
 COPY pkgs/* /opt/conda/pkgs/
-COPY conda-bld /opt/conda/conda-bld
+COPY conda-bld/linux-64/${CONDA_PKG} /opt/conda/conda-bld/linux-64
 
 #RUN conda config --set always_yes yes --set changeps1 no
 #RUN conda config --add channels r
@@ -18,4 +18,4 @@ COPY conda-bld /opt/conda/conda-bld
 #RUN conda config --add channels bioconda
 #RUN conda config --add channels nyuad-cgsb
 #
-# conda config --add channels file://anaconda-conda-bld/linux-64
+#conda config --add channels file://opt/conda/conda-bld/linux-64
diff --git a/scripts/travis-run-conda-build-all.sh b/scripts/travis-run-conda-build-all.sh
index 69be0a5..35aabf7 100644
--- a/scripts/travis-run-conda-build-all.sh
+++ b/scripts/travis-run-conda-build-all.sh
@@ -44,6 +44,7 @@ ls -lahR $CONDA_BLD_PATH
 
 cp Dockerfile /opt/anaconda3
 cd /opt/anaconda3
+docker build --build-arg CONDA_PKG='gencore_rnaseq-1.0-r3.4.1_1.tar.bz2' -t 'gencore_rnaseq:1.0-r3.4.1_1'
 
 docker images
 set +x

From a0cb6655721bebaa29e35f2d601219b73f4bb922 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 10:00:59 +0400
Subject: [PATCH 28/45] trying again

---
 scripts/travis-setup.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh
index 28b1bfa..dc1f645 100755
--- a/scripts/travis-setup.sh
+++ b/scripts/travis-setup.sh
@@ -30,8 +30,8 @@ sudo chown -R $USER /opt/anaconda3
 sudo chown -R $USER /anaconda
 
 wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
-bash miniconda.sh -b -p /anaconda3
-export PATH="/anaconda3/bin:$PATH"
+bash miniconda.sh -b -p /anaconda
+export PATH="/anaconda/bin:$PATH"
 hash -r
 conda config --set always_yes yes --set changeps1 no
 conda config --add channels r

From d48195777cba66ac6ea4f670673b80b4d1620363 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 10:20:36 +0400
Subject: [PATCH 29/45] quiet wget

---
 scripts/travis-setup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh
index dc1f645..0f46f0d 100755
--- a/scripts/travis-setup.sh
+++ b/scripts/travis-setup.sh
@@ -29,7 +29,7 @@ sudo mkdir /anaconda
 sudo chown -R $USER /opt/anaconda3
 sudo chown -R $USER /anaconda
 
-wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh --quiet -O miniconda.sh
 bash miniconda.sh -b -p /anaconda
 export PATH="/anaconda/bin:$PATH"
 hash -r

From e70acd67408700e8a58f9cc4427a1f48827caedb Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 10:27:14 +0400
Subject: [PATCH 30/45] just install it to home

---
 scripts/travis-setup.sh | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh
index 0f46f0d..69db1dc 100755
--- a/scripts/travis-setup.sh
+++ b/scripts/travis-setup.sh
@@ -30,15 +30,15 @@ sudo chown -R $USER /opt/anaconda3
 sudo chown -R $USER /anaconda
 
 wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh --quiet -O miniconda.sh
-bash miniconda.sh -b -p /anaconda
-export PATH="/anaconda/bin:$PATH"
+bash miniconda.sh -b -p /home/travis/anaconda3
+export PATH="/home/travis/anaconda3/bin:$PATH"
 hash -r
 conda config --set always_yes yes --set changeps1 no
 conda config --add channels r
 conda config --add channels conda-forge
 conda config --add channels bioconda
 
-/anaconda/bin/conda index /anaconda/conda-bld/linux-64 /anaconda/conda-bld/osx-64
-/anaconda/bin/conda config --add channels file://anaconda/conda-bld
-/anaconda/bin/conda install -y r-base r-essentials openjdk perl bioconductor-biobase nodejs
-/anaconda/bin/npm install -g marked-man
+conda index /anaconda/conda-bld/linux-64 /anaconda/conda-bld/osx-64
+conda config --add channels file://anaconda/conda-bld
+conda install -y r-base r-essentials openjdk perl bioconductor-biobase nodejs
+npm install -g marked-man

From 1fb00fb9a67836f45b432f6c102c6a3ab021075a Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 10:28:41 +0400
Subject: [PATCH 31/45] more cleanup

---
 scripts/travis-setup.sh | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh
index 69db1dc..8940238 100755
--- a/scripts/travis-setup.sh
+++ b/scripts/travis-setup.sh
@@ -24,10 +24,8 @@ done
 SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 
 pip install pyyaml
-sudo mkdir /anaconda
 
 sudo chown -R $USER /opt/anaconda3
-sudo chown -R $USER /anaconda
 
 wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh --quiet -O miniconda.sh
 bash miniconda.sh -b -p /home/travis/anaconda3
@@ -37,8 +35,9 @@ conda config --set always_yes yes --set changeps1 no
 conda config --add channels r
 conda config --add channels conda-forge
 conda config --add channels bioconda
+conda config --add channels nyuad-cgsb
 
-conda index /anaconda/conda-bld/linux-64 /anaconda/conda-bld/osx-64
-conda config --add channels file://anaconda/conda-bld
+conda index /home/travis/anaconda3/conda-bld/linux-64 /home/travis/anaconda3/conda-bld/osx-64
+conda config --add channels file://home/travis/anaconda3/conda-bld
 conda install -y r-base r-essentials openjdk perl bioconductor-biobase nodejs
 npm install -g marked-man

From 83e737c7b180c617029e16e2c316cb9a80494e03 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 10:53:07 +0400
Subject: [PATCH 32/45] no index?

---
 scripts/travis-setup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh
index 8940238..4ebec4f 100755
--- a/scripts/travis-setup.sh
+++ b/scripts/travis-setup.sh
@@ -37,7 +37,7 @@ conda config --add channels conda-forge
 conda config --add channels bioconda
 conda config --add channels nyuad-cgsb
 
-conda index /home/travis/anaconda3/conda-bld/linux-64 /home/travis/anaconda3/conda-bld/osx-64
+# conda index /home/travis/anaconda3/conda-bld/linux-64
 conda config --add channels file://home/travis/anaconda3/conda-bld
 conda install -y r-base r-essentials openjdk perl bioconductor-biobase nodejs
 npm install -g marked-man

From ed5dd061848e70ad05347a8e089909b6845c5668 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 11:05:47 +0400
Subject: [PATCH 33/45] commiting

---
 scripts/travis-run-conda-build-all.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/travis-run-conda-build-all.sh b/scripts/travis-run-conda-build-all.sh
index 35aabf7..3591c22 100644
--- a/scripts/travis-run-conda-build-all.sh
+++ b/scripts/travis-run-conda-build-all.sh
@@ -20,7 +20,6 @@ then
     exit 0
 fi
 
-export PATH=/anaconda/bin:$PATH
 
 # TODO Add another upload
 if [[ ( $TRAVIS_BRANCH == "master" || $TRAVIS_BRANCH == "bulk" ) && "$TRAVIS_PULL_REQUEST" == "false" && $TRAVIS_REPO_SLUG == "$MY_TRAVIS_REPO_SLUG" ]]
@@ -38,6 +37,8 @@ then
 fi
 
 set -x
+
+export PATH=/home/travis/anaconda3/bin:$PATH
 conda install -y conda-build-all
 conda-build-all recipes --inspect-channels nyuad-cgsb $UPLOAD_ARG
 ls -lahR $CONDA_BLD_PATH

From 8bc9143f4ace98b520286f9c0ce511ea2a9c0adc Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 11:13:48 +0400
Subject: [PATCH 34/45] it wasn't executable darn

---
 scripts/travis-run-conda-build-all.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 scripts/travis-run-conda-build-all.sh

diff --git a/scripts/travis-run-conda-build-all.sh b/scripts/travis-run-conda-build-all.sh
old mode 100644
new mode 100755

From ba20db2867d73cd02ab5be8e344a8c3a9270a4da Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 11:45:57 +0400
Subject: [PATCH 35/45] bah

---
 scripts/travis-run-conda-build-all.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/travis-run-conda-build-all.sh b/scripts/travis-run-conda-build-all.sh
index 3591c22..fa6afe8 100755
--- a/scripts/travis-run-conda-build-all.sh
+++ b/scripts/travis-run-conda-build-all.sh
@@ -8,6 +8,7 @@ set +u
 [[ -z $RANGE_ARG ]] && RANGE_ARG="--git-range master HEAD"
 [[ -z $DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK  ]] && DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK="false"
 [[ -z $SKIP_LINTING ]] && SKIP_LINTING=false
+[[ -z $UPLOAD_ARG ]] && UPLOAD_ARG=""
 set -u
 
 if [[ $TRAVIS_BRANCH != "master" && $TRAVIS_BRANCH != "bulk" && $TRAVIS_PULL_REQUEST == "false" && $TRAVIS_REPO_SLUG == "$MY_TRAVIS_REPO_SLUG" ]]

From 4c2c03a72c8143861e6ff5a3e7cd799d952852e3 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 12:02:52 +0400
Subject: [PATCH 36/45] adding in some conda build args

---
 .travis.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 186e566..abcba99 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -25,6 +25,18 @@ env:
   - CONTAINER_NAMESPACE: 'nyuad_cgsb'
   - CONDA_PKGS_DIRS: '/opt/anaconda3/pkgs'
   - CONDA_BLD_PATH: '/opt/anaconda3/conda-bld'
+  - CONDA_R: '3.4.1'
+  - CONDA_PERL: '5.22.0'
+  - CONDA_HTSLIB: "1.6"
+  - CONDA_BOOST: "1.64"
+  - CONDA_NPY: "112"
+  - CONDA_NCURSES: "5.9"
+  - CONDA_GSL: "1.16"
+  - CONDA_GMP: "5.1"
+  - CONDA_HDF5: "1.8.17"
+  - CONDA_ZLIB: "1.2.8"
+  - CONDA_BZIP2: "1.0"
+  - CONDA_XZ: "5.2"
   # - SUBDAGS=1
   # - BIOCONDA_UTILS_TAG=master
   # - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=debug"

From 9b134fe14368a3b7a99e086fedecea4b7fd34dcc Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 12:03:32 +0400
Subject: [PATCH 37/45] removing build

---
 scripts/travis-run-conda-build-all.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/travis-run-conda-build-all.sh b/scripts/travis-run-conda-build-all.sh
index fa6afe8..fbfa604 100755
--- a/scripts/travis-run-conda-build-all.sh
+++ b/scripts/travis-run-conda-build-all.sh
@@ -46,7 +46,7 @@ ls -lahR $CONDA_BLD_PATH
 
 cp Dockerfile /opt/anaconda3
 cd /opt/anaconda3
-docker build --build-arg CONDA_PKG='gencore_rnaseq-1.0-r3.4.1_1.tar.bz2' -t 'gencore_rnaseq:1.0-r3.4.1_1'
+docker build --build-arg CONDA_PKG='gencore_rnaseq-1.0-r3.4.1_1.tar.bz2'
 
 docker images
 set +x

From 01e5bad506a8393e7898489f8910bec4b63b9449 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 13:26:54 +0400
Subject: [PATCH 38/45] try try again

---
 scripts/travis-run-conda-build-all.sh | 4 +++-
 scripts/travis-setup.sh               | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/scripts/travis-run-conda-build-all.sh b/scripts/travis-run-conda-build-all.sh
index fbfa604..7c32cbf 100755
--- a/scripts/travis-run-conda-build-all.sh
+++ b/scripts/travis-run-conda-build-all.sh
@@ -44,9 +44,11 @@ conda install -y conda-build-all
 conda-build-all recipes --inspect-channels nyuad-cgsb $UPLOAD_ARG
 ls -lahR $CONDA_BLD_PATH
 
+echo "We should be building things now...."
+
 cp Dockerfile /opt/anaconda3
 cd /opt/anaconda3
-docker build --build-arg CONDA_PKG='gencore_rnaseq-1.0-r3.4.1_1.tar.bz2'
+travis_wait 30 docker build --build-arg CONDA_PKG='gencore_rnaseq-1.0-r3.4.1_1.tar.bz2'
 
 docker images
 set +x
diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh
index 4ebec4f..5be81e0 100755
--- a/scripts/travis-setup.sh
+++ b/scripts/travis-setup.sh
@@ -38,6 +38,6 @@ conda config --add channels bioconda
 conda config --add channels nyuad-cgsb
 
 # conda index /home/travis/anaconda3/conda-bld/linux-64
-conda config --add channels file://home/travis/anaconda3/conda-bld
+# conda config --add channels file://home/travis/anaconda3/conda-bld
 conda install -y r-base r-essentials openjdk perl bioconductor-biobase nodejs
 npm install -g marked-man

From a7493b27de9c93fab24e7fe07ebe358f5fe31caf Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 13:53:26 +0400
Subject: [PATCH 39/45] baaaah travis times out

---
 recipes/gencore_rnaseq/1.0/meta.yaml  | 34 +++++++++++++--------------
 scripts/travis-run-conda-build-all.sh |  2 +-
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index 0323b20..06ce4e8 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -14,24 +14,24 @@ requirements:
   ##Alignment
   - samtools ==1.3.1
   - kallisto ==0.43.0
-  - cufflinks-patch ==2.2.1
-  - bowtie2 ==2.2.8
-  - tophat ==2.1.0
-  - star ==2.5.2a
-  - bcftools ==1.3.1
-  - blat ==35
-  - gatk ==3.6
-  - picard ==2.5.0
-  - prinseq ==0.20.4
-  - vcftools ==0.1.14
-  - bedtools ==2.25.0
-  - vcflib ==1.0.0_rc1
-  - bamtools ==2.4.0
-  - seqtk ==1.2
+  # - cufflinks-patch ==2.2.1
+  # - bowtie2 ==2.2.8
+  # - tophat ==2.1.0
+  # - star ==2.5.2a
+  # - bcftools ==1.3.1
+  # - blat ==35
+  # - gatk ==3.6
+  # - picard ==2.5.0
+  # - prinseq ==0.20.4
+  # - vcftools ==0.1.14
+  # - bedtools ==2.25.0
+  # - vcflib ==1.0.0_rc1
+  # - bamtools ==2.4.0
+  # - seqtk ==1.2
   ##Downstream processing
-  - r-base
-  - r-essentials
-  - r-cairo
+  # - r-base
+  # - r-essentials
+  # - r-cairo
   # - bioconductor-deseq2
   # - bioconductor-edger >=3.14.0
   # - bioconductor-cummerbund >=2.16.0
diff --git a/scripts/travis-run-conda-build-all.sh b/scripts/travis-run-conda-build-all.sh
index 7c32cbf..ec8a7a7 100755
--- a/scripts/travis-run-conda-build-all.sh
+++ b/scripts/travis-run-conda-build-all.sh
@@ -41,7 +41,7 @@ set -x
 
 export PATH=/home/travis/anaconda3/bin:$PATH
 conda install -y conda-build-all
-conda-build-all recipes --inspect-channels nyuad-cgsb $UPLOAD_ARG
+travis_wait 30 conda-build-all recipes --inspect-channels nyuad-cgsb $UPLOAD_ARG
 ls -lahR $CONDA_BLD_PATH
 
 echo "We should be building things now...."

From 57552ee950f1eb3e430b4667435e2fff7e7b1b0c Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 14:08:48 +0400
Subject: [PATCH 40/45] WHERE IST HE TRAVIS WAIT

---
 .travis.yml                           | 4 ++--
 scripts/travis-run-conda-build-all.sh | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index abcba99..85b13bc 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,11 +11,11 @@ jobs:
   - stage: Linux
     if: "(type = push) AND ((branch IN (master, bulk)) OR (fork = true))"
     os: linux
-    script: scripts/travis-run-conda-build-all.sh
+    script: travis_wait 30 scripts/travis-run-conda-build-all.sh
   - stage: Linux
     if: type = pull_request
     os: linux
-    script: scripts/travis-run-conda-build-all.sh
+    script: travis_wait 30 scripts/travis-run-conda-build-all.sh
 env:
   global:
   - MINICONDA_VER: '4.3.21'
diff --git a/scripts/travis-run-conda-build-all.sh b/scripts/travis-run-conda-build-all.sh
index ec8a7a7..48c1cf8 100755
--- a/scripts/travis-run-conda-build-all.sh
+++ b/scripts/travis-run-conda-build-all.sh
@@ -41,14 +41,14 @@ set -x
 
 export PATH=/home/travis/anaconda3/bin:$PATH
 conda install -y conda-build-all
-travis_wait 30 conda-build-all recipes --inspect-channels nyuad-cgsb $UPLOAD_ARG
+conda-build-all recipes --inspect-channels nyuad-cgsb $UPLOAD_ARG
 ls -lahR $CONDA_BLD_PATH
 
 echo "We should be building things now...."
 
 cp Dockerfile /opt/anaconda3
 cd /opt/anaconda3
-travis_wait 30 docker build --build-arg CONDA_PKG='gencore_rnaseq-1.0-r3.4.1_1.tar.bz2'
+docker build --build-arg CONDA_PKG='gencore_rnaseq-1.0-r3.4.1_1.tar.bz2'
 
 docker images
 set +x

From 71962d147ca962c56c1588c8b6d029d88571bea7 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 14:21:17 +0400
Subject: [PATCH 41/45] stupid docker build

---
 scripts/travis-run-conda-build-all.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/travis-run-conda-build-all.sh b/scripts/travis-run-conda-build-all.sh
index 48c1cf8..baad27a 100755
--- a/scripts/travis-run-conda-build-all.sh
+++ b/scripts/travis-run-conda-build-all.sh
@@ -48,7 +48,7 @@ echo "We should be building things now...."
 
 cp Dockerfile /opt/anaconda3
 cd /opt/anaconda3
-docker build --build-arg CONDA_PKG='gencore_rnaseq-1.0-r3.4.1_1.tar.bz2'
+docker build --build-arg CONDA_PKG='gencore_rnaseq-1.0-r3.4.1_1.tar.bz2' .
 
 docker images
 set +x

From afca61fbf5f77961bd77e8d81e7379d10dc48214 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 14:21:47 +0400
Subject: [PATCH 42/45] lets try this

---
 scripts/travis-run-conda-build-all.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/travis-run-conda-build-all.sh b/scripts/travis-run-conda-build-all.sh
index baad27a..b077c0b 100755
--- a/scripts/travis-run-conda-build-all.sh
+++ b/scripts/travis-run-conda-build-all.sh
@@ -48,7 +48,7 @@ echo "We should be building things now...."
 
 cp Dockerfile /opt/anaconda3
 cd /opt/anaconda3
-docker build --build-arg CONDA_PKG='gencore_rnaseq-1.0-r3.4.1_1.tar.bz2' .
+docker build --build-arg CONDA_PKG='gencore_rnaseq-1.0-r3.4.1_1.tar.bz2' -t 'gencore_rnaseq:1.0-r3.4.1_1' .
 
 docker images
 set +x

From 02d9cba078e43032e7f063cc2d367d1aee020ccb Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 14:22:43 +0400
Subject: [PATCH 43/45] need R for build string

---
 recipes/gencore_rnaseq/1.0/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
index 06ce4e8..743c9db 100644
--- a/recipes/gencore_rnaseq/1.0/meta.yaml
+++ b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -29,7 +29,7 @@ requirements:
   # - bamtools ==2.4.0
   # - seqtk ==1.2
   ##Downstream processing
-  # - r-base
+  - r-base
   # - r-essentials
   # - r-cairo
   # - bioconductor-deseq2

From 02950555d203d83f186eb0be189f8279be12fe7e Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 14:41:20 +0400
Subject: [PATCH 44/45] try the whole dockerfile workflow

---
 Dockerfile | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index c13d24b..0830168 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -12,10 +12,11 @@ RUN mkdir -p /opt/conda/conda-bld/linux-64
 COPY pkgs/* /opt/conda/pkgs/
 COPY conda-bld/linux-64/${CONDA_PKG} /opt/conda/conda-bld/linux-64
 
-#RUN conda config --set always_yes yes --set changeps1 no
-#RUN conda config --add channels r
-#RUN conda config --add channels conda-forge
-#RUN conda config --add channels bioconda
-#RUN conda config --add channels nyuad-cgsb
-#
-#conda config --add channels file://opt/conda/conda-bld/linux-64
+RUN conda config --set always_yes yes --set changeps1 no
+RUN conda config --add channels r
+RUN conda config --add channels conda-forge
+RUN conda config --add channels bioconda
+RUN conda config --add channels nyuad-cgsb
+
+RUN conda config --add channels file://opt/conda/conda-bld/linux-64
+RUN conda install -y --use-local gencore_rnaseq 

From b4a4f1b2fef438e590c1f1f946f4f21c961b7b39 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Wed, 13 Dec 2017 15:09:26 +0400
Subject: [PATCH 45/45] index the channel

---
 Dockerfile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 0830168..880e846 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -18,5 +18,7 @@ RUN conda config --add channels conda-forge
 RUN conda config --add channels bioconda
 RUN conda config --add channels nyuad-cgsb
 
+RUN ls -lah /opt/conda/conda-bld/linux-64
 RUN conda config --add channels file://opt/conda/conda-bld/linux-64
-RUN conda install -y --use-local gencore_rnaseq 
+RUN conda index /opt/conda/conda-bld/linux-64
+RUN conda install -y --use-local gencore_rnaseq