diff --git a/src/singularity_modules/bcftools/1.7/bcftools b/src/singularity_modules/bcftools/1.7/bcftools new file mode 100644 index 0000000000000000000000000000000000000000..0b6dd7dd2c3fcf8e4d37bdf285bb4caefa1aaf51 --- /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 0000000000000000000000000000000000000000..33f7309a610e53d7db01ae2f14ecae3f7b5b9756 --- /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 0000000000000000000000000000000000000000..af1106ffe9bca165c12eb784b570d5eb736a4ac3 --- /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 0000000000000000000000000000000000000000..9b4503234b30626d0668bfd619d9243e0814a103 --- /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 0000000000000000000000000000000000000000..e8c41bdc8af82fee3cce41f0f6496f21b55704be --- /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 0000000000000000000000000000000000000000..cf69e9236b4760843073281fc4311a1507a3201a --- /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 0000000000000000000000000000000000000000..fa7348ae17fe786286fc0be73d3c3faf6604d932 --- /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 0000000000000000000000000000000000000000..362bda98bd24973e0a517e9baed1a4c3b3505945 --- /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 0000000000000000000000000000000000000000..71f969248e0aa79fb0cea9dc24eb756aae1acaee --- /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 0000000000000000000000000000000000000000..e653e488281d4a0c0f556ba672e159d4aa3a5dcd --- /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 0000000000000000000000000000000000000000..4053b759aaa1bc3b33fe0ab5ceef1b1c32f440dd --- /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 0000000000000000000000000000000000000000..ffecc35fed3de3dd88832fc1f621898ccd957c01 --- /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 0000000000000000000000000000000000000000..cc0d2213cbf7e723bcf76d788c5e6d617e6317d6 --- /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 0000000000000000000000000000000000000000..1da370ad5ecf6eabaa3321ff8b4bee5d3cfd909e --- /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 0000000000000000000000000000000000000000..2eccd8be1780e951ed61ebfb2e294dc596336cf6 --- /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 0000000000000000000000000000000000000000..d16d21b6cca2901f323af7a57e6f96394c2c75a3 --- /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 0000000000000000000000000000000000000000..e8282a1ee8d4eab71440c2943f4d1876b1012c2d --- /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 0000000000000000000000000000000000000000..0c4ab6f90b1cc818b8b12a4fbf8b77b8051a07be --- /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 0000000000000000000000000000000000000000..df87417d41360cd13c6adcaf02ef91ca81978ad6 --- /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 0000000000000000000000000000000000000000..f7be0c13925dfbe3ac6560ad27d53f6d837b3cc5 --- /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 0000000000000000000000000000000000000000..27ad1732154be9cf7b44d6a7881e704d88c0907f --- /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 0000000000000000000000000000000000000000..b6f899fb77933047db8f2ae06cf5c8aeea4b8fc7 --- /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 0000000000000000000000000000000000000000..230104ddcb6a688d962fb1aa1bc0309202a06652 --- /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 0000000000000000000000000000000000000000..00743e8cd8a4fcf679d8138897c76da601ccae34 --- /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 0000000000000000000000000000000000000000..fe772f25e652e7694adf8bc618a81d1832a20ade --- /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 0000000000000000000000000000000000000000..19b4bb3baa30d87651716fbd07d05b5f35dd8359 --- /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 0000000000000000000000000000000000000000..47d5cd4cc118d198b7d619670114a3f376100812 --- /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 0000000000000000000000000000000000000000..8578c72689205a3ddb9cd95d73be23f4ca0ce31e --- /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 0000000000000000000000000000000000000000..e7321e510b98ddd1aced59ce5841f3dd10e8a086 --- /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 0000000000000000000000000000000000000000..35b6aa7294bf723e51c477d4b4d23b1b80a249a0 --- /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 0000000000000000000000000000000000000000..57100d993e0cd5737be2ddfb4412296c4b2e9077 --- /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 0000000000000000000000000000000000000000..d811b276612bd32babbdca75c57b1fd769f7b7ba --- /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 0000000000000000000000000000000000000000..6f87648a9109a83560c6182e72223d587b64a767 --- /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 0000000000000000000000000000000000000000..382bf0440aae90eccd045fc7b07a27af6ba6743c --- /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 0000000000000000000000000000000000000000..44bb8bb85f9bd3162dde41d25f1f80fa9c5c94b3 --- /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 0000000000000000000000000000000000000000..8511bddfaa7faba56d022d33dbeedeca5058198d --- /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 0000000000000000000000000000000000000000..344b13431f15bb2d11dbf9a7d69321bb9890412f --- /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 0000000000000000000000000000000000000000..673c53e23a82eacd1aeeed2dfef8be2ad0fd7949 --- /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 0000000000000000000000000000000000000000..924beee1d8a6cd0c432b1c6a791fb87123cd3697 --- /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 $@