From 950e35f1d159809c4818ef34319f038ef4ee9e02 Mon Sep 17 00:00:00 2001 From: Laurent Modolo <laurent.modolo@ens-lyon.fr> Date: Tue, 16 Apr 2019 10:45:00 +0200 Subject: [PATCH] add .sh helpers for singularity on the ccin2p3 --- src/singularity_modules/bcftools/1.7/bcftools | 2 ++ src/singularity_modules/bedtools/2.25.0/bedtools | 2 ++ src/singularity_modules/bioawk/1.0/bioawk | 2 ++ src/singularity_modules/bowtie/1.2.2/bowtie | 2 ++ src/singularity_modules/bowtie2/2.3.4.1/bowtie2 | 2 ++ src/singularity_modules/bwa/0.7.17/bwa | 2 ++ src/singularity_modules/canu/1.6/canu | 2 ++ src/singularity_modules/cutadapt/1.14/cutadapt | 2 ++ src/singularity_modules/cutadapt/1.15/cutadapt | 2 ++ src/singularity_modules/cutadapt/2.1/cutadapt | 2 ++ src/singularity_modules/deeptools/3.0.2/deeptools | 2 ++ src/singularity_modules/deeptools/3.1.1/deeptools | 2 ++ src/singularity_modules/fastp/0.19.7/fastp | 2 ++ src/singularity_modules/fastqc/0.11.5/fastqc | 2 ++ src/singularity_modules/file_handle/0.1.1/file_handle | 2 ++ src/singularity_modules/gatk/4.0.8.1/gatk | 2 ++ src/singularity_modules/hisat2/2.0.0/hisat2 | 2 ++ src/singularity_modules/hisat2/2.1.0/hisat2 | 2 ++ src/singularity_modules/htseq/0.11.2/htseq | 2 ++ src/singularity_modules/htseq/0.8.0/htseq | 2 ++ src/singularity_modules/kallisto/0.43.1/kallisto | 2 ++ src/singularity_modules/macs2/2.1.2/macs2 | 2 ++ src/singularity_modules/multiqc/1.0/multiqc | 2 ++ src/singularity_modules/multiqc/1.7/multiqc | 2 ++ src/singularity_modules/music/6613c53/music | 2 ++ src/singularity_modules/picard/2.18.11/picard | 2 ++ src/singularity_modules/pigz/2.4/pigz | 2 ++ src/singularity_modules/rsem/1.3.0/rsem | 2 ++ src/singularity_modules/salmon/0.8.2/salmon | 2 ++ src/singularity_modules/sambamba/0.6.7/sambamba | 2 ++ src/singularity_modules/samblaster/0.1.24/samblaster | 2 ++ src/singularity_modules/samtools/1.7/samtools | 2 ++ src/singularity_modules/sratoolkit/2.8.2/sratoolkit | 2 ++ src/singularity_modules/subread/1.6.4/subread | 2 ++ src/singularity_modules/tophat/2.1.1/tophat | 2 ++ src/singularity_modules/trimmomatic/0.36/trimmomatic | 2 ++ src/singularity_modules/ucsc/375/ucsc | 2 ++ src/singularity_modules/umi_tools/1.0.0/umi_tools | 2 ++ src/singularity_modules/urqt/d62c1f8/urqt | 2 ++ 39 files changed, 78 insertions(+) create mode 100644 src/singularity_modules/bcftools/1.7/bcftools create mode 100644 src/singularity_modules/bedtools/2.25.0/bedtools create mode 100644 src/singularity_modules/bioawk/1.0/bioawk create mode 100644 src/singularity_modules/bowtie/1.2.2/bowtie create mode 100644 src/singularity_modules/bowtie2/2.3.4.1/bowtie2 create mode 100644 src/singularity_modules/bwa/0.7.17/bwa create mode 100644 src/singularity_modules/canu/1.6/canu create mode 100644 src/singularity_modules/cutadapt/1.14/cutadapt create mode 100644 src/singularity_modules/cutadapt/1.15/cutadapt create mode 100644 src/singularity_modules/cutadapt/2.1/cutadapt create mode 100644 src/singularity_modules/deeptools/3.0.2/deeptools create mode 100644 src/singularity_modules/deeptools/3.1.1/deeptools create mode 100644 src/singularity_modules/fastp/0.19.7/fastp create mode 100644 src/singularity_modules/fastqc/0.11.5/fastqc create mode 100644 src/singularity_modules/file_handle/0.1.1/file_handle create mode 100644 src/singularity_modules/gatk/4.0.8.1/gatk create mode 100644 src/singularity_modules/hisat2/2.0.0/hisat2 create mode 100644 src/singularity_modules/hisat2/2.1.0/hisat2 create mode 100644 src/singularity_modules/htseq/0.11.2/htseq create mode 100644 src/singularity_modules/htseq/0.8.0/htseq create mode 100644 src/singularity_modules/kallisto/0.43.1/kallisto create mode 100644 src/singularity_modules/macs2/2.1.2/macs2 create mode 100644 src/singularity_modules/multiqc/1.0/multiqc create mode 100644 src/singularity_modules/multiqc/1.7/multiqc create mode 100644 src/singularity_modules/music/6613c53/music create mode 100644 src/singularity_modules/picard/2.18.11/picard create mode 100644 src/singularity_modules/pigz/2.4/pigz create mode 100644 src/singularity_modules/rsem/1.3.0/rsem create mode 100644 src/singularity_modules/salmon/0.8.2/salmon create mode 100644 src/singularity_modules/sambamba/0.6.7/sambamba create mode 100644 src/singularity_modules/samblaster/0.1.24/samblaster create mode 100644 src/singularity_modules/samtools/1.7/samtools create mode 100644 src/singularity_modules/sratoolkit/2.8.2/sratoolkit create mode 100644 src/singularity_modules/subread/1.6.4/subread create mode 100644 src/singularity_modules/tophat/2.1.1/tophat create mode 100644 src/singularity_modules/trimmomatic/0.36/trimmomatic create mode 100644 src/singularity_modules/ucsc/375/ucsc create mode 100644 src/singularity_modules/umi_tools/1.0.0/umi_tools create mode 100644 src/singularity_modules/urqt/d62c1f8/urqt diff --git a/src/singularity_modules/bcftools/1.7/bcftools b/src/singularity_modules/bcftools/1.7/bcftools new file mode 100644 index 00000000..0b6dd7dd --- /dev/null +++ b/src/singularity_modules/bcftools/1.7/bcftools @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/bcftools:1.7.img bcftools $@ diff --git a/src/singularity_modules/bedtools/2.25.0/bedtools b/src/singularity_modules/bedtools/2.25.0/bedtools new file mode 100644 index 00000000..33f7309a --- /dev/null +++ b/src/singularity_modules/bedtools/2.25.0/bedtools @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/bedtools:2.25.0.img bedtools $@ diff --git a/src/singularity_modules/bioawk/1.0/bioawk b/src/singularity_modules/bioawk/1.0/bioawk new file mode 100644 index 00000000..af1106ff --- /dev/null +++ b/src/singularity_modules/bioawk/1.0/bioawk @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/bioawk:1.0.img bioawk $@ diff --git a/src/singularity_modules/bowtie/1.2.2/bowtie b/src/singularity_modules/bowtie/1.2.2/bowtie new file mode 100644 index 00000000..9b450323 --- /dev/null +++ b/src/singularity_modules/bowtie/1.2.2/bowtie @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/bowtie:1.2.2.img bowtie $@ diff --git a/src/singularity_modules/bowtie2/2.3.4.1/bowtie2 b/src/singularity_modules/bowtie2/2.3.4.1/bowtie2 new file mode 100644 index 00000000..e8c41bdc --- /dev/null +++ b/src/singularity_modules/bowtie2/2.3.4.1/bowtie2 @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/bowtie2:2.3.4.1.img bowtie2 $@ diff --git a/src/singularity_modules/bwa/0.7.17/bwa b/src/singularity_modules/bwa/0.7.17/bwa new file mode 100644 index 00000000..cf69e923 --- /dev/null +++ b/src/singularity_modules/bwa/0.7.17/bwa @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/bwa:0.7.17.img bwa $@ diff --git a/src/singularity_modules/canu/1.6/canu b/src/singularity_modules/canu/1.6/canu new file mode 100644 index 00000000..fa7348ae --- /dev/null +++ b/src/singularity_modules/canu/1.6/canu @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/canu:1.6.img canu $@ diff --git a/src/singularity_modules/cutadapt/1.14/cutadapt b/src/singularity_modules/cutadapt/1.14/cutadapt new file mode 100644 index 00000000..362bda98 --- /dev/null +++ b/src/singularity_modules/cutadapt/1.14/cutadapt @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/cutadapt:1.14.img cutadapt $@ diff --git a/src/singularity_modules/cutadapt/1.15/cutadapt b/src/singularity_modules/cutadapt/1.15/cutadapt new file mode 100644 index 00000000..71f96924 --- /dev/null +++ b/src/singularity_modules/cutadapt/1.15/cutadapt @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/cutadapt:1.15.img cutadapt $@ diff --git a/src/singularity_modules/cutadapt/2.1/cutadapt b/src/singularity_modules/cutadapt/2.1/cutadapt new file mode 100644 index 00000000..e653e488 --- /dev/null +++ b/src/singularity_modules/cutadapt/2.1/cutadapt @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/cutadapt:2.1.img cutadapt $@ diff --git a/src/singularity_modules/deeptools/3.0.2/deeptools b/src/singularity_modules/deeptools/3.0.2/deeptools new file mode 100644 index 00000000..4053b759 --- /dev/null +++ b/src/singularity_modules/deeptools/3.0.2/deeptools @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/deeptools:3.0.2.img deeptools $@ diff --git a/src/singularity_modules/deeptools/3.1.1/deeptools b/src/singularity_modules/deeptools/3.1.1/deeptools new file mode 100644 index 00000000..ffecc35f --- /dev/null +++ b/src/singularity_modules/deeptools/3.1.1/deeptools @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/deeptools:3.1.1.img deeptools $@ diff --git a/src/singularity_modules/fastp/0.19.7/fastp b/src/singularity_modules/fastp/0.19.7/fastp new file mode 100644 index 00000000..cc0d2213 --- /dev/null +++ b/src/singularity_modules/fastp/0.19.7/fastp @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/fastp:0.19.7.img fastp $@ diff --git a/src/singularity_modules/fastqc/0.11.5/fastqc b/src/singularity_modules/fastqc/0.11.5/fastqc new file mode 100644 index 00000000..1da370ad --- /dev/null +++ b/src/singularity_modules/fastqc/0.11.5/fastqc @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/fastqc:0.11.5.img fastqc $@ diff --git a/src/singularity_modules/file_handle/0.1.1/file_handle b/src/singularity_modules/file_handle/0.1.1/file_handle new file mode 100644 index 00000000..2eccd8be --- /dev/null +++ b/src/singularity_modules/file_handle/0.1.1/file_handle @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/file_handle:0.1.1.img file_handle $@ diff --git a/src/singularity_modules/gatk/4.0.8.1/gatk b/src/singularity_modules/gatk/4.0.8.1/gatk new file mode 100644 index 00000000..d16d21b6 --- /dev/null +++ b/src/singularity_modules/gatk/4.0.8.1/gatk @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/gatk:4.0.8.1.img gatk $@ diff --git a/src/singularity_modules/hisat2/2.0.0/hisat2 b/src/singularity_modules/hisat2/2.0.0/hisat2 new file mode 100644 index 00000000..e8282a1e --- /dev/null +++ b/src/singularity_modules/hisat2/2.0.0/hisat2 @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/hisat2:2.0.0.img hisat2 $@ diff --git a/src/singularity_modules/hisat2/2.1.0/hisat2 b/src/singularity_modules/hisat2/2.1.0/hisat2 new file mode 100644 index 00000000..0c4ab6f9 --- /dev/null +++ b/src/singularity_modules/hisat2/2.1.0/hisat2 @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/hisat2:2.1.0.img hisat2 $@ diff --git a/src/singularity_modules/htseq/0.11.2/htseq b/src/singularity_modules/htseq/0.11.2/htseq new file mode 100644 index 00000000..df87417d --- /dev/null +++ b/src/singularity_modules/htseq/0.11.2/htseq @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/htseq:0.11.2.img htseq $@ diff --git a/src/singularity_modules/htseq/0.8.0/htseq b/src/singularity_modules/htseq/0.8.0/htseq new file mode 100644 index 00000000..f7be0c13 --- /dev/null +++ b/src/singularity_modules/htseq/0.8.0/htseq @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/htseq:0.8.0.img htseq $@ diff --git a/src/singularity_modules/kallisto/0.43.1/kallisto b/src/singularity_modules/kallisto/0.43.1/kallisto new file mode 100644 index 00000000..27ad1732 --- /dev/null +++ b/src/singularity_modules/kallisto/0.43.1/kallisto @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/kallisto:0.43.1.img kallisto $@ diff --git a/src/singularity_modules/macs2/2.1.2/macs2 b/src/singularity_modules/macs2/2.1.2/macs2 new file mode 100644 index 00000000..b6f899fb --- /dev/null +++ b/src/singularity_modules/macs2/2.1.2/macs2 @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/macs2:2.1.2.img macs2 $@ diff --git a/src/singularity_modules/multiqc/1.0/multiqc b/src/singularity_modules/multiqc/1.0/multiqc new file mode 100644 index 00000000..230104dd --- /dev/null +++ b/src/singularity_modules/multiqc/1.0/multiqc @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/multiqc:1.0.img multiqc $@ diff --git a/src/singularity_modules/multiqc/1.7/multiqc b/src/singularity_modules/multiqc/1.7/multiqc new file mode 100644 index 00000000..00743e8c --- /dev/null +++ b/src/singularity_modules/multiqc/1.7/multiqc @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/multiqc:1.7.img multiqc $@ diff --git a/src/singularity_modules/music/6613c53/music b/src/singularity_modules/music/6613c53/music new file mode 100644 index 00000000..fe772f25 --- /dev/null +++ b/src/singularity_modules/music/6613c53/music @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/music:6613c53.img music $@ diff --git a/src/singularity_modules/picard/2.18.11/picard b/src/singularity_modules/picard/2.18.11/picard new file mode 100644 index 00000000..19b4bb3b --- /dev/null +++ b/src/singularity_modules/picard/2.18.11/picard @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/picard:2.18.11.img picard $@ diff --git a/src/singularity_modules/pigz/2.4/pigz b/src/singularity_modules/pigz/2.4/pigz new file mode 100644 index 00000000..47d5cd4c --- /dev/null +++ b/src/singularity_modules/pigz/2.4/pigz @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/pigz:2.4.img pigz $@ diff --git a/src/singularity_modules/rsem/1.3.0/rsem b/src/singularity_modules/rsem/1.3.0/rsem new file mode 100644 index 00000000..8578c726 --- /dev/null +++ b/src/singularity_modules/rsem/1.3.0/rsem @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/rsem:1.3.0.img rsem $@ diff --git a/src/singularity_modules/salmon/0.8.2/salmon b/src/singularity_modules/salmon/0.8.2/salmon new file mode 100644 index 00000000..e7321e51 --- /dev/null +++ b/src/singularity_modules/salmon/0.8.2/salmon @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/salmon:0.8.2.img salmon $@ diff --git a/src/singularity_modules/sambamba/0.6.7/sambamba b/src/singularity_modules/sambamba/0.6.7/sambamba new file mode 100644 index 00000000..35b6aa72 --- /dev/null +++ b/src/singularity_modules/sambamba/0.6.7/sambamba @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/sambamba:0.6.7.img sambamba $@ diff --git a/src/singularity_modules/samblaster/0.1.24/samblaster b/src/singularity_modules/samblaster/0.1.24/samblaster new file mode 100644 index 00000000..57100d99 --- /dev/null +++ b/src/singularity_modules/samblaster/0.1.24/samblaster @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/samblaster:0.1.24.img samblaster $@ diff --git a/src/singularity_modules/samtools/1.7/samtools b/src/singularity_modules/samtools/1.7/samtools new file mode 100644 index 00000000..d811b276 --- /dev/null +++ b/src/singularity_modules/samtools/1.7/samtools @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/samtools:1.7.img samtools $@ diff --git a/src/singularity_modules/sratoolkit/2.8.2/sratoolkit b/src/singularity_modules/sratoolkit/2.8.2/sratoolkit new file mode 100644 index 00000000..6f87648a --- /dev/null +++ b/src/singularity_modules/sratoolkit/2.8.2/sratoolkit @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/sratoolkit:2.8.2.img sratoolkit $@ diff --git a/src/singularity_modules/subread/1.6.4/subread b/src/singularity_modules/subread/1.6.4/subread new file mode 100644 index 00000000..382bf044 --- /dev/null +++ b/src/singularity_modules/subread/1.6.4/subread @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/subread:1.6.4.img subread $@ diff --git a/src/singularity_modules/tophat/2.1.1/tophat b/src/singularity_modules/tophat/2.1.1/tophat new file mode 100644 index 00000000..44bb8bb8 --- /dev/null +++ b/src/singularity_modules/tophat/2.1.1/tophat @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/tophat:2.1.1.img tophat $@ diff --git a/src/singularity_modules/trimmomatic/0.36/trimmomatic b/src/singularity_modules/trimmomatic/0.36/trimmomatic new file mode 100644 index 00000000..8511bddf --- /dev/null +++ b/src/singularity_modules/trimmomatic/0.36/trimmomatic @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/trimmomatic:0.36.img trimmomatic $@ diff --git a/src/singularity_modules/ucsc/375/ucsc b/src/singularity_modules/ucsc/375/ucsc new file mode 100644 index 00000000..344b1343 --- /dev/null +++ b/src/singularity_modules/ucsc/375/ucsc @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/ucsc:375.img ucsc $@ diff --git a/src/singularity_modules/umi_tools/1.0.0/umi_tools b/src/singularity_modules/umi_tools/1.0.0/umi_tools new file mode 100644 index 00000000..673c53e2 --- /dev/null +++ b/src/singularity_modules/umi_tools/1.0.0/umi_tools @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/umi_tools:1.0.0.img umi_tools $@ diff --git a/src/singularity_modules/urqt/d62c1f8/urqt b/src/singularity_modules/urqt/d62c1f8/urqt new file mode 100644 index 00000000..924beee1 --- /dev/null +++ b/src/singularity_modules/urqt/d62c1f8/urqt @@ -0,0 +1,2 @@ +#/bin/bash +singularity exec /sps/lbmc/common/singularity/urqt:d62c1f8.img urqt $@ -- GitLab