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_metagenomics/1.0/meta.yaml b/recipes/gencore_metagenomics/1.0/meta.yaml new file mode 100644 index 0000000..a225805 --- /dev/null +++ b/recipes/gencore_metagenomics/1.0/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "gencore_metagenomics" %} +{% set version = "1.0" %} + + +package: + name: {{ name }} + version: {{ version }} + +build: + number: 0 + skip: True # [osx] + +requirements: + run: + - blat ==35 + - cd-hit ==4.6.4 + - augustus ==3.2.2 + - blast ==2.2.31 + - hmmer ==3.1b2 + - bwa ==0.7.15 + - samtools ==1.3.1 + - bcftools ==1.3.1 + - bedtools ==2.25.0 + - vcftools ==0.1.14 + - vcflib ==1.0.0_rc1 + - bamtools ==2.4.0 + - mawk ==1.3.4 + - seqtk ==1.2 + - pear ==0.9.6 + - bowtie2 ==2.2.8 + - bioconductor-dada2 ==1.0.3 + - mothur ==1.36.1 + +test: + commands: + - samtools --help 2>&1 | grep 'samtools' + +about: + home: 'https://cgsb.abudhabi.nyu.edu/' + license: BSD + summary: 'Gencore Metagenomics' diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml deleted file mode 100644 index 945b6a1..0000000 --- a/recipes/gencore_rnaseq/1.0/meta.yaml +++ /dev/null @@ -1,54 +0,0 @@ -{% 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'