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Feature/rnaseq #2

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Feature/rnaseq #2

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4f3d71e
Merge branch 'feature/variant_detection' into develop
jerowe Nov 16, 2017
3eaaa47
Merge branch 'master' of github.com:biosails/bioconda-recipes into de…
jerowe Nov 16, 2017
0bb82a3
adding rnaseq
jerowe Nov 16, 2017
355823a
adding nyuad-cgsb channel must put new cufflinks in bioconda
jerowe Nov 16, 2017
a2a2e7c
commit
jerowe Nov 16, 2017
a78ffaa
trying to get rnaseq working
jerowe Nov 16, 2017
2ee79ee
Merge branch 'master' of github.com:biosails/bioconda-recipes into fe…
jerowe Nov 20, 2017
1b0dbd2
build gencore rnaseq module
jerowe Nov 20, 2017
46d31ed
adding in travis cache
jerowe Nov 20, 2017
25b3bf7
make sure we are caching the right dir
jerowe Nov 20, 2017
7615f13
more checks for package cache
jerowe Nov 20, 2017
9a9126d
conda info
jerowe Nov 20, 2017
1efbbee
trying with the cache again
jerowe Nov 20, 2017
ccc0a99
this one
jerowe Nov 20, 2017
f66d5e9
test recipe
jerowe Nov 20, 2017
4fd158a
stupid conflict
jerowe Nov 20, 2017
fa0dfb0
adding more things to cache
jerowe Nov 20, 2017
800f980
whyyyy no cache
jerowe Nov 20, 2017
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1 change: 1 addition & 0 deletions config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,3 +13,4 @@ channels:
- bioconda
- conda-forge
- defaults
- nyuad-cgsb
Binary file removed involucro
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55 changes: 55 additions & 0 deletions recipes/gencore_rnaseq/1.0/meta.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,55 @@
{% set name = "gencore_rnaseq" %}
{% set version = "1.0" %}


package:
name: {{ name }}
version: {{ version }}

build:
number: 0
skip: True # [osx]

requirements:
run:
- samtools ==1.3.1
- bcftools ==1.3.1
- kallisto ==0.43.0
- 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
- 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:
- bowtie2 --help 2>&1 | grep 'bowtie'

about:
home: 'https://cgsb.abudhabi.nyu.edu/'
license: BSD
summary: 'Gencore RnaSeq Module'
7 changes: 6 additions & 1 deletion scripts/travis-setup.sh
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Expand Up @@ -3,6 +3,11 @@ set -e
set -x


echo "#################### Begin Checking the cache! ##########################"
ls -lah /home/travis/.conda/pkgs
echo "#################### End Checking the cache! ##########################"


if [[ $TRAVIS_BRANCH != "master" && $TRAVIS_BRANCH != "bulk" && $TRAVIS_PULL_REQUEST == "false" && $TRAVIS_REPO_SLUG == "$MY_TRAVIS_REPO_SLUG" ]]
then
echo ""
Expand All @@ -29,7 +34,7 @@ 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 install -y r-base r-essentials openjdk perl bioconductor-biobase salmon kallisto

/anaconda/bin/conda info
ls -lah /home/travis/.conda/pkgs