From 3efd91bd170fbe88d904c5775e5890f8e7248069 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 6 Nov 2019 17:02:04 +0100
Subject: [PATCH] hide src/* files not necessary for users

---
 .gitmodules                                                     | 2 +-
 src/{conda_packages.sh => .conda_packages.sh}                   | 0
 src/{docker_modules => .docker_modules}/bcftools/1.7/Dockerfile | 0
 .../bcftools/1.7/docker_init.sh                                 | 0
 .../bedtools/2.25.0/Dockerfile                                  | 0
 .../bedtools/2.25.0/docker_init.sh                              | 0
 src/{docker_modules => .docker_modules}/bioawk/1.0/Dockerfile   | 0
 .../bioawk/1.0/docker_init.sh                                   | 0
 src/{docker_modules => .docker_modules}/bowtie/1.2.2/Dockerfile | 0
 .../bowtie/1.2.2/docker_init.sh                                 | 0
 .../bowtie2/2.3.4.1/Dockerfile                                  | 0
 .../bowtie2/2.3.4.1/docker_init.sh                              | 0
 src/{docker_modules => .docker_modules}/bwa/0.7.17/Dockerfile   | 0
 .../bwa/0.7.17/docker_init.sh                                   | 0
 src/{docker_modules => .docker_modules}/canu/1.6/Dockerfile     | 0
 src/{docker_modules => .docker_modules}/canu/1.6/docker_init.sh | 0
 .../cutadapt/1.14/Dockerfile                                    | 0
 .../cutadapt/1.14/docker_init.sh                                | 0
 .../cutadapt/1.15/Dockerfile                                    | 0
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 src/{docker_modules => .docker_modules}/cutadapt/2.1/Dockerfile | 0
 .../cutadapt/2.1/docker_init.sh                                 | 0
 .../deeptools/3.0.2/Dockerfile                                  | 0
 .../deeptools/3.0.2/docker_init.sh                              | 0
 .../deeptools/3.1.1/Dockerfile                                  | 0
 .../deeptools/3.1.1/docker_init.sh                              | 0
 src/{docker_modules => .docker_modules}/docker_push.sh          | 0
 src/{docker_modules => .docker_modules}/docker_update.sh        | 0
 src/{docker_modules => .docker_modules}/fastp/0.19.7/Dockerfile | 0
 .../fastp/0.19.7/docker_init.sh                                 | 0
 .../fastqc/0.11.5/Dockerfile                                    | 0
 .../fastqc/0.11.5/docker_init.sh                                | 0
 .../file_handle/0.1.1/Dockerfile                                | 0
 .../file_handle/0.1.1/docker_init.sh                            | 0
 src/{docker_modules => .docker_modules}/gatk/4.0.8.1/Dockerfile | 0
 .../gatk/4.0.8.1/docker_init.sh                                 | 0
 src/{docker_modules => .docker_modules}/hisat2/2.0.0/Dockerfile | 0
 .../hisat2/2.0.0/docker_init.sh                                 | 0
 src/{docker_modules => .docker_modules}/hisat2/2.1.0/Dockerfile | 0
 .../hisat2/2.1.0/docker_init.sh                                 | 0
 src/{docker_modules => .docker_modules}/htseq/0.11.2/Dockerfile | 0
 .../htseq/0.11.2/docker_init.sh                                 | 0
 src/{docker_modules => .docker_modules}/htseq/0.8.0/Dockerfile  | 0
 .../htseq/0.8.0/docker_init.sh                                  | 0
 .../kallisto/0.43.1/Dockerfile                                  | 0
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 .../kallisto/0.44.0/Dockerfile                                  | 0
 .../kallisto/0.44.0/docker_init.sh                              | 0
 src/{docker_modules => .docker_modules}/macs2/2.1.2/Dockerfile  | 0
 .../macs2/2.1.2/docker_init.sh                                  | 0
 src/{docker_modules => .docker_modules}/multiqc/1.0/Dockerfile  | 0
 .../multiqc/1.0/docker_init.sh                                  | 0
 src/{docker_modules => .docker_modules}/multiqc/1.7/Dockerfile  | 0
 .../multiqc/1.7/docker_init.sh                                  | 0
 .../music/6613c53/Dockerfile                                    | 0
 .../music/6613c53/docker_init.sh                                | 0
 .../picard/2.18.11/Dockerfile                                   | 0
 .../picard/2.18.11/PicardCommandLine                            | 0
 .../picard/2.18.11/docker_init.sh                               | 0
 src/{docker_modules => .docker_modules}/pigz/2.4/Dockerfile     | 0
 src/{docker_modules => .docker_modules}/pigz/2.4/docker_init.sh | 0
 src/{docker_modules => .docker_modules}/python/3.8/Dockerfile   | 0
 .../python/3.8/docker_init.sh                                   | 0
 src/{docker_modules => .docker_modules}/r/3.5.3/Dockerfile      | 0
 src/{docker_modules => .docker_modules}/r/3.5.3/docker_init.sh  | 0
 src/{docker_modules => .docker_modules}/rsem/1.3.0/Dockerfile   | 0
 .../rsem/1.3.0/docker_init.sh                                   | 0
 src/{docker_modules => .docker_modules}/salmon/0.8.2/Dockerfile | 0
 .../salmon/0.8.2/docker_init.sh                                 | 0
 .../sambamba/0.6.7/Dockerfile                                   | 0
 .../sambamba/0.6.7/docker_init.sh                               | 0
 .../sambamba/0.6.9/Dockerfile                                   | 0
 .../sambamba/0.6.9/docker_init.sh                               | 0
 .../samblaster/0.1.24/Dockerfile                                | 0
 .../samblaster/0.1.24/docker_init.sh                            | 0
 src/{docker_modules => .docker_modules}/samtools/1.7/Dockerfile | 0
 .../samtools/1.7/docker_init.sh                                 | 0
 .../sratoolkit/2.8.2/Dockerfile                                 | 0
 .../sratoolkit/2.8.2/docker_init.sh                             | 0
 .../subread/1.6.4/Dockerfile                                    | 0
 .../subread/1.6.4/docker_init.sh                                | 0
 src/{docker_modules => .docker_modules}/tophat/2.1.1/Dockerfile | 0
 .../tophat/2.1.1/docker_init.sh                                 | 0
 .../trimmomatic/0.36/Dockerfile                                 | 0
 .../trimmomatic/0.36/docker_init.sh                             | 0
 src/{docker_modules => .docker_modules}/ucsc/375/Dockerfile     | 0
 src/{docker_modules => .docker_modules}/ucsc/375/docker_init.sh | 0
 .../umi_tools/0.5.4/Dockerfile                                  | 0
 .../umi_tools/0.5.4/docker_init.sh                              | 0
 .../umi_tools/1.0.0/Dockerfile                                  | 0
 .../umi_tools/1.0.0/docker_init.sh                              | 0
 src/{docker_modules => .docker_modules}/urqt/d62c1f8/Dockerfile | 0
 .../urqt/d62c1f8/docker_init.sh                                 | 0
 src/{psmn_modules => .psmn_modules}                             | 0
 .../bcftools/1.7/bcftools                                       | 0
 .../bcftools/1.7/bcftools.def                                   | 0
 .../bcftools/1.7/build.sh                                       | 0
 .../bedtools/2.25.0/bedtools                                    | 0
 .../bedtools/2.25.0/bedtools.def                                | 0
 .../bedtools/2.25.0/build.sh                                    | 0
 .../bioawk/1.0/bioawk                                           | 0
 .../bioawk/1.0/bioawk.def                                       | 0
 .../bioawk/1.0/build.sh                                         | 0
 .../bowtie/1.2.2/bowtie                                         | 0
 .../bowtie/1.2.2/bowtie.def                                     | 0
 .../bowtie/1.2.2/build.sh                                       | 0
 .../bowtie2/2.3.4.1/bowtie2                                     | 0
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 .../bowtie2/2.3.4.1/build.sh                                    | 0
 .../bwa/0.7.17/build.sh                                         | 0
 .../bwa/0.7.17/bwa                                              | 0
 .../bwa/0.7.17/bwa.def                                          | 0
 .../canu/1.6/build.sh                                           | 0
 src/{singularity_modules => .singularity_modules}/canu/1.6/canu | 0
 .../canu/1.6/canu.def                                           | 0
 .../cutadapt/1.14/build.sh                                      | 0
 .../cutadapt/1.14/cutadapt                                      | 0
 .../cutadapt/1.14/cutadapt.def                                  | 0
 .../cutadapt/1.15/build.sh                                      | 0
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 .../cutadapt/2.1/build.sh                                       | 0
 .../cutadapt/2.1/cutadapt                                       | 0
 .../cutadapt/2.1/cutadapt.def                                   | 0
 .../deeptools/3.0.2/build.sh                                    | 0
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 .../deeptools/3.1.1/build.sh                                    | 0
 .../deeptools/3.1.1/deeptools                                   | 0
 .../deeptools/3.1.1/deeptools.def                               | 0
 .../docker_to_singularity.sh                                    | 0
 .../fastp/0.19.7/build.sh                                       | 0
 .../fastp/0.19.7/fastp                                          | 0
 .../fastp/0.19.7/fastp.def                                      | 0
 .../fastqc/0.11.5/build.sh                                      | 0
 .../fastqc/0.11.5/fastqc                                        | 0
 .../fastqc/0.11.5/fastqc.def                                    | 0
 .../file_handle/0.1.1/build.sh                                  | 0
 .../file_handle/0.1.1/file_handle                               | 0
 .../file_handle/0.1.1/file_handle.def                           | 0
 .../gatk/4.0.8.1/build.sh                                       | 0
 .../gatk/4.0.8.1/gatk                                           | 0
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 .../hisat2/2.0.0/build.sh                                       | 0
 .../hisat2/2.0.0/hisat2                                         | 0
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 .../hisat2/2.1.0/hisat2                                         | 0
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 .../htseq/0.11.2/build.sh                                       | 0
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 .../htseq/0.8.0/build.sh                                        | 0
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 .../htseq/0.8.0/htseq.def                                       | 0
 .../kallisto/0.43.1/build.sh                                    | 0
 .../kallisto/0.43.1/kallisto                                    | 0
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 .../kallisto/0.44.0/build.sh                                    | 0
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 .../macs2/2.1.2/build.sh                                        | 0
 .../macs2/2.1.2/macs2                                           | 0
 .../macs2/2.1.2/macs2.def                                       | 0
 .../multiqc/1.0/build.sh                                        | 0
 .../multiqc/1.0/multiqc                                         | 0
 .../multiqc/1.0/multiqc.def                                     | 0
 .../multiqc/1.7/build.sh                                        | 0
 .../multiqc/1.7/multiqc                                         | 0
 .../multiqc/1.7/multiqc.def                                     | 0
 .../music/6613c53/build.sh                                      | 0
 .../music/6613c53/music                                         | 0
 .../music/6613c53/music.def                                     | 0
 .../picard/2.18.11/PicardCommandLine                            | 0
 .../picard/2.18.11/build.sh                                     | 0
 .../picard/2.18.11/picard                                       | 0
 .../picard/2.18.11/picard.def                                   | 0
 .../pigz/2.4/build.sh                                           | 0
 src/{singularity_modules => .singularity_modules}/pigz/2.4/pigz | 0
 .../pigz/2.4/pigz.def                                           | 0
 .../r/3.5.3/build.sh                                            | 0
 src/{singularity_modules => .singularity_modules}/r/3.5.3/r     | 0
 src/{singularity_modules => .singularity_modules}/r/3.5.3/r.def | 0
 .../rsem/1.3.0/build.sh                                         | 0
 .../rsem/1.3.0/rsem                                             | 0
 .../rsem/1.3.0/rsem.def                                         | 0
 .../salmon/0.8.2/build.sh                                       | 0
 .../salmon/0.8.2/salmon                                         | 0
 .../salmon/0.8.2/salmon.def                                     | 0
 .../sambamba/0.6.7/build.sh                                     | 0
 .../sambamba/0.6.7/sambamba                                     | 0
 .../sambamba/0.6.7/sambamba.def                                 | 0
 .../sambamba/0.6.9/build.sh                                     | 0
 .../sambamba/0.6.9/sambamba                                     | 0
 .../sambamba/0.6.9/sambamba.def                                 | 0
 .../samblaster/0.1.24/build.sh                                  | 0
 .../samblaster/0.1.24/samblaster                                | 0
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 .../samtools/1.7/build.sh                                       | 0
 .../samtools/1.7/samtools                                       | 0
 .../samtools/1.7/samtools.def                                   | 0
 .../sratoolkit/2.8.2/build.sh                                   | 0
 .../sratoolkit/2.8.2/sratoolkit                                 | 0
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 .../subread/1.6.4/build.sh                                      | 0
 .../subread/1.6.4/subread                                       | 0
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 .../tophat/2.1.1/build.sh                                       | 0
 .../tophat/2.1.1/tophat                                         | 0
 .../tophat/2.1.1/tophat.def                                     | 0
 .../trimmomatic/0.36/build.sh                                   | 0
 .../trimmomatic/0.36/trimmomatic                                | 0
 .../trimmomatic/0.36/trimmomatic.def                            | 0
 .../ucsc/375/build.sh                                           | 0
 src/{singularity_modules => .singularity_modules}/ucsc/375/ucsc | 0
 .../ucsc/375/ucsc.def                                           | 0
 .../umi_tools/1.0.0/build.sh                                    | 0
 .../umi_tools/1.0.0/umi_tools                                   | 0
 .../umi_tools/1.0.0/umi_tools.def                               | 0
 .../urqt/d62c1f8/build.sh                                       | 0
 .../urqt/d62c1f8/urqt                                           | 0
 .../urqt/d62c1f8/urqt.def                                       | 0
 src/{update_tools.sh => .update_tools.sh}                       | 0
 223 files changed, 1 insertion(+), 1 deletion(-)
 rename src/{conda_packages.sh => .conda_packages.sh} (100%)
 rename src/{docker_modules => .docker_modules}/bcftools/1.7/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/bcftools/1.7/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/bedtools/2.25.0/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/bedtools/2.25.0/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/bioawk/1.0/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/bioawk/1.0/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/bowtie/1.2.2/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/bowtie/1.2.2/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/bowtie2/2.3.4.1/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/bowtie2/2.3.4.1/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/bwa/0.7.17/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/bwa/0.7.17/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/canu/1.6/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/canu/1.6/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/cutadapt/1.14/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/cutadapt/1.14/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/cutadapt/1.15/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/cutadapt/1.15/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/cutadapt/2.1/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/cutadapt/2.1/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/deeptools/3.0.2/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/deeptools/3.0.2/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/deeptools/3.1.1/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/deeptools/3.1.1/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/docker_push.sh (100%)
 rename src/{docker_modules => .docker_modules}/docker_update.sh (100%)
 rename src/{docker_modules => .docker_modules}/fastp/0.19.7/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/fastp/0.19.7/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/fastqc/0.11.5/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/fastqc/0.11.5/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/file_handle/0.1.1/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/file_handle/0.1.1/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/gatk/4.0.8.1/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/gatk/4.0.8.1/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/hisat2/2.0.0/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/hisat2/2.0.0/docker_init.sh (100%)
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 rename src/{docker_modules => .docker_modules}/hisat2/2.1.0/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/htseq/0.11.2/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/htseq/0.11.2/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/htseq/0.8.0/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/htseq/0.8.0/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/kallisto/0.43.1/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/kallisto/0.43.1/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/kallisto/0.44.0/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/kallisto/0.44.0/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/macs2/2.1.2/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/macs2/2.1.2/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/multiqc/1.0/Dockerfile (100%)
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 rename src/{docker_modules => .docker_modules}/multiqc/1.7/Dockerfile (100%)
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 rename src/{docker_modules => .docker_modules}/picard/2.18.11/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/picard/2.18.11/PicardCommandLine (100%)
 rename src/{docker_modules => .docker_modules}/picard/2.18.11/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/pigz/2.4/Dockerfile (100%)
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 rename src/{docker_modules => .docker_modules}/rsem/1.3.0/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/rsem/1.3.0/docker_init.sh (100%)
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 rename src/{docker_modules => .docker_modules}/salmon/0.8.2/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/sambamba/0.6.7/Dockerfile (100%)
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 rename src/{docker_modules => .docker_modules}/trimmomatic/0.36/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/ucsc/375/Dockerfile (100%)
 rename src/{docker_modules => .docker_modules}/ucsc/375/docker_init.sh (100%)
 rename src/{docker_modules => .docker_modules}/umi_tools/0.5.4/Dockerfile (100%)
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 rename src/{psmn_modules => .psmn_modules} (100%)
 rename src/{singularity_modules => .singularity_modules}/bcftools/1.7/bcftools (100%)
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 rename src/{singularity_modules => .singularity_modules}/bcftools/1.7/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/bedtools/2.25.0/bedtools (100%)
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 rename src/{singularity_modules => .singularity_modules}/bedtools/2.25.0/build.sh (100%)
 rename src/{singularity_modules => .singularity_modules}/bioawk/1.0/bioawk (100%)
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 rename src/{singularity_modules => .singularity_modules}/bowtie/1.2.2/bowtie (100%)
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diff --git a/.gitmodules b/.gitmodules
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--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "src/sge_modules"]
-	path = src/psmn_modules
+	path = src/.psmn_modules
 	url = gitlab_lbmc:PSMN/modules.git
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