From bfdcf56e9fe8c41de2849e5c7ad15a5f72430cd6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 5 Mar 2019 15:36:43 +0100
Subject: [PATCH] change tools name to lowercase

---
 apps/{BCFtools => bcftools}/install_1.7.sh        | 0
 apps/{BEDtools => bedtools}/install_2.25.0.sh     | 0
 apps/{Bowtie2 => bowtie2}/install_2.3.2.sh        | 0
 apps/{Bowtie2 => bowtie2}/install_2.3.4.1.sh      | 0
 apps/{CDHIT => cdhit}/install_4.6.8.sh            | 0
 apps/{deepTools => deeptools}/install_3.0.2.sh    | 0
 apps/{FastQC => fastqc}/install_0.11.5.sh         | 0
 apps/{GATK => gatk}/install_4.0.10.1.sh           | 0
 apps/{HTSeq => htseq}/install_0.8.0.sh            | 0
 apps/{HTSeq => htseq}/install_0.9.1.sh            | 0
 apps/{Kallisto => kallisto}/install_0.43.1.sh     | 0
 apps/{Kallisto => kallisto}/install_0.44.0.sh     | 0
 apps/{MultiQC => multiqc}/install_0.9.sh          | 0
 apps/{MultiQC => multiqc}/install_1.0.sh          | 0
 apps/{MUSIC => music}/install_6613c53.sh          | 0
 apps/{RSEM => rsem}/install_1.3.0.sh              | 0
 apps/{RSEM => rsem}/install_1.3.1.sh              | 0
 apps/{Salmon => salmon}/install_0.8.2.sh          | 0
 apps/{SAMtools => samtools}/install_1.5.sh        | 0
 apps/{SAMtools => samtools}/install_1.7.sh        | 0
 apps/{SRAtoolkit => sratoolkit}/install_2.8.2.sh  | 0
 apps/{TopHat => tophat}/install_2.1.1.sh          | 0
 apps/{Trimmomatic => trimmomatic}/install_0.36.sh | 0
 apps/{UrQt => urqt}/install_d62c1f8.sh            | 0
 modulefiles/{BCFtools => bcftools}/1.7.lua        | 0
 modulefiles/{BEDtools => bedtools}/2.25.0.lua     | 0
 modulefiles/{Bowtie2 => bowtie2}/2.3.2.lua        | 0
 modulefiles/{Bowtie2 => bowtie2}/2.3.4.1.lua      | 0
 modulefiles/{CDHIT => cdhit}/4.6.8                | 0
 modulefiles/{deepTools => deeptools}/3.0.2.lua    | 0
 modulefiles/{FastQC => fastqc}/0.11.5.lua         | 0
 modulefiles/{GATK => gatk}/4.0.10.1.lua           | 0
 modulefiles/{GCC => gcc}/4.9.4.lua                | 0
 modulefiles/{GCC => gcc}/5.4.0.lua                | 0
 modulefiles/{GCC => gcc}/6.4.0.lua                | 0
 modulefiles/{GCC => gcc}/7.2.0.lua                | 0
 modulefiles/{GCC => gcc}/default                  | 0
 modulefiles/{HTSeq => htseq}/0.8.0.lua            | 0
 modulefiles/{HTSeq => htseq}/0.9.1.lua            | 0
 modulefiles/{Java => java}/1.7.0_21.lua           | 0
 modulefiles/{Java => java}/1.7.0_71.lua           | 0
 modulefiles/{Java => java}/1.8.0_151.lua          | 0
 modulefiles/{Kallisto => kallisto}/0.43.1.lua     | 0
 modulefiles/{Kallisto => kallisto}/0.44.0.lua     | 0
 modulefiles/{MACS2 => macs2}/2.1.1.20160309.lua   | 0
 modulefiles/{MultiQC => multiqc}/0.9              | 0
 modulefiles/{MultiQC => multiqc}/1.0.lua          | 0
 modulefiles/{MUSIC => music}/6613c53.lua          | 0
 modulefiles/{Python => python}/2.7.13.lua         | 0
 modulefiles/{Python => python}/3.6.1.lua          | 0
 modulefiles/{R => r}/3.2.4.lua                    | 0
 modulefiles/{R => r}/3.4.3.lua                    | 0
 modulefiles/{RSEM => rsem}/1.3.0.lua              | 0
 modulefiles/{RSEM => rsem}/1.3.1.lua              | 0
 modulefiles/{Salmon => salmon}/0.8.2.lua          | 0
 modulefiles/{SAMtools => samtools}/1.5.lua        | 0
 modulefiles/{SAMtools => samtools}/1.7.lua        | 0
 modulefiles/{SRAtoolkit => sratoolkit}/2.8.2.lua  | 0
 modulefiles/{TopHat => tophat}/2.1.1.lua          | 0
 modulefiles/{Trimmomatic => trimmomatic}/0.37.lua | 0
 modulefiles/{UrQt => urqt}/d62c1f8.lua            | 0
 61 files changed, 0 insertions(+), 0 deletions(-)
 rename apps/{BCFtools => bcftools}/install_1.7.sh (100%)
 rename apps/{BEDtools => bedtools}/install_2.25.0.sh (100%)
 rename apps/{Bowtie2 => bowtie2}/install_2.3.2.sh (100%)
 rename apps/{Bowtie2 => bowtie2}/install_2.3.4.1.sh (100%)
 rename apps/{CDHIT => cdhit}/install_4.6.8.sh (100%)
 rename apps/{deepTools => deeptools}/install_3.0.2.sh (100%)
 rename apps/{FastQC => fastqc}/install_0.11.5.sh (100%)
 rename apps/{GATK => gatk}/install_4.0.10.1.sh (100%)
 rename apps/{HTSeq => htseq}/install_0.8.0.sh (100%)
 rename apps/{HTSeq => htseq}/install_0.9.1.sh (100%)
 rename apps/{Kallisto => kallisto}/install_0.43.1.sh (100%)
 rename apps/{Kallisto => kallisto}/install_0.44.0.sh (100%)
 rename apps/{MultiQC => multiqc}/install_0.9.sh (100%)
 rename apps/{MultiQC => multiqc}/install_1.0.sh (100%)
 rename apps/{MUSIC => music}/install_6613c53.sh (100%)
 rename apps/{RSEM => rsem}/install_1.3.0.sh (100%)
 rename apps/{RSEM => rsem}/install_1.3.1.sh (100%)
 rename apps/{Salmon => salmon}/install_0.8.2.sh (100%)
 rename apps/{SAMtools => samtools}/install_1.5.sh (100%)
 rename apps/{SAMtools => samtools}/install_1.7.sh (100%)
 rename apps/{SRAtoolkit => sratoolkit}/install_2.8.2.sh (100%)
 rename apps/{TopHat => tophat}/install_2.1.1.sh (100%)
 rename apps/{Trimmomatic => trimmomatic}/install_0.36.sh (100%)
 rename apps/{UrQt => urqt}/install_d62c1f8.sh (100%)
 rename modulefiles/{BCFtools => bcftools}/1.7.lua (100%)
 rename modulefiles/{BEDtools => bedtools}/2.25.0.lua (100%)
 rename modulefiles/{Bowtie2 => bowtie2}/2.3.2.lua (100%)
 rename modulefiles/{Bowtie2 => bowtie2}/2.3.4.1.lua (100%)
 rename modulefiles/{CDHIT => cdhit}/4.6.8 (100%)
 rename modulefiles/{deepTools => deeptools}/3.0.2.lua (100%)
 rename modulefiles/{FastQC => fastqc}/0.11.5.lua (100%)
 rename modulefiles/{GATK => gatk}/4.0.10.1.lua (100%)
 rename modulefiles/{GCC => gcc}/4.9.4.lua (100%)
 rename modulefiles/{GCC => gcc}/5.4.0.lua (100%)
 rename modulefiles/{GCC => gcc}/6.4.0.lua (100%)
 rename modulefiles/{GCC => gcc}/7.2.0.lua (100%)
 rename modulefiles/{GCC => gcc}/default (100%)
 rename modulefiles/{HTSeq => htseq}/0.8.0.lua (100%)
 rename modulefiles/{HTSeq => htseq}/0.9.1.lua (100%)
 rename modulefiles/{Java => java}/1.7.0_21.lua (100%)
 rename modulefiles/{Java => java}/1.7.0_71.lua (100%)
 rename modulefiles/{Java => java}/1.8.0_151.lua (100%)
 rename modulefiles/{Kallisto => kallisto}/0.43.1.lua (100%)
 rename modulefiles/{Kallisto => kallisto}/0.44.0.lua (100%)
 rename modulefiles/{MACS2 => macs2}/2.1.1.20160309.lua (100%)
 rename modulefiles/{MultiQC => multiqc}/0.9 (100%)
 rename modulefiles/{MultiQC => multiqc}/1.0.lua (100%)
 rename modulefiles/{MUSIC => music}/6613c53.lua (100%)
 rename modulefiles/{Python => python}/2.7.13.lua (100%)
 rename modulefiles/{Python => python}/3.6.1.lua (100%)
 rename modulefiles/{R => r}/3.2.4.lua (100%)
 rename modulefiles/{R => r}/3.4.3.lua (100%)
 rename modulefiles/{RSEM => rsem}/1.3.0.lua (100%)
 rename modulefiles/{RSEM => rsem}/1.3.1.lua (100%)
 rename modulefiles/{Salmon => salmon}/0.8.2.lua (100%)
 rename modulefiles/{SAMtools => samtools}/1.5.lua (100%)
 rename modulefiles/{SAMtools => samtools}/1.7.lua (100%)
 rename modulefiles/{SRAtoolkit => sratoolkit}/2.8.2.lua (100%)
 rename modulefiles/{TopHat => tophat}/2.1.1.lua (100%)
 rename modulefiles/{Trimmomatic => trimmomatic}/0.37.lua (100%)
 rename modulefiles/{UrQt => urqt}/d62c1f8.lua (100%)

diff --git a/apps/BCFtools/install_1.7.sh b/apps/bcftools/install_1.7.sh
similarity index 100%
rename from apps/BCFtools/install_1.7.sh
rename to apps/bcftools/install_1.7.sh
diff --git a/apps/BEDtools/install_2.25.0.sh b/apps/bedtools/install_2.25.0.sh
similarity index 100%
rename from apps/BEDtools/install_2.25.0.sh
rename to apps/bedtools/install_2.25.0.sh
diff --git a/apps/Bowtie2/install_2.3.2.sh b/apps/bowtie2/install_2.3.2.sh
similarity index 100%
rename from apps/Bowtie2/install_2.3.2.sh
rename to apps/bowtie2/install_2.3.2.sh
diff --git a/apps/Bowtie2/install_2.3.4.1.sh b/apps/bowtie2/install_2.3.4.1.sh
similarity index 100%
rename from apps/Bowtie2/install_2.3.4.1.sh
rename to apps/bowtie2/install_2.3.4.1.sh
diff --git a/apps/CDHIT/install_4.6.8.sh b/apps/cdhit/install_4.6.8.sh
similarity index 100%
rename from apps/CDHIT/install_4.6.8.sh
rename to apps/cdhit/install_4.6.8.sh
diff --git a/apps/deepTools/install_3.0.2.sh b/apps/deeptools/install_3.0.2.sh
similarity index 100%
rename from apps/deepTools/install_3.0.2.sh
rename to apps/deeptools/install_3.0.2.sh
diff --git a/apps/FastQC/install_0.11.5.sh b/apps/fastqc/install_0.11.5.sh
similarity index 100%
rename from apps/FastQC/install_0.11.5.sh
rename to apps/fastqc/install_0.11.5.sh
diff --git a/apps/GATK/install_4.0.10.1.sh b/apps/gatk/install_4.0.10.1.sh
similarity index 100%
rename from apps/GATK/install_4.0.10.1.sh
rename to apps/gatk/install_4.0.10.1.sh
diff --git a/apps/HTSeq/install_0.8.0.sh b/apps/htseq/install_0.8.0.sh
similarity index 100%
rename from apps/HTSeq/install_0.8.0.sh
rename to apps/htseq/install_0.8.0.sh
diff --git a/apps/HTSeq/install_0.9.1.sh b/apps/htseq/install_0.9.1.sh
similarity index 100%
rename from apps/HTSeq/install_0.9.1.sh
rename to apps/htseq/install_0.9.1.sh
diff --git a/apps/Kallisto/install_0.43.1.sh b/apps/kallisto/install_0.43.1.sh
similarity index 100%
rename from apps/Kallisto/install_0.43.1.sh
rename to apps/kallisto/install_0.43.1.sh
diff --git a/apps/Kallisto/install_0.44.0.sh b/apps/kallisto/install_0.44.0.sh
similarity index 100%
rename from apps/Kallisto/install_0.44.0.sh
rename to apps/kallisto/install_0.44.0.sh
diff --git a/apps/MultiQC/install_0.9.sh b/apps/multiqc/install_0.9.sh
similarity index 100%
rename from apps/MultiQC/install_0.9.sh
rename to apps/multiqc/install_0.9.sh
diff --git a/apps/MultiQC/install_1.0.sh b/apps/multiqc/install_1.0.sh
similarity index 100%
rename from apps/MultiQC/install_1.0.sh
rename to apps/multiqc/install_1.0.sh
diff --git a/apps/MUSIC/install_6613c53.sh b/apps/music/install_6613c53.sh
similarity index 100%
rename from apps/MUSIC/install_6613c53.sh
rename to apps/music/install_6613c53.sh
diff --git a/apps/RSEM/install_1.3.0.sh b/apps/rsem/install_1.3.0.sh
similarity index 100%
rename from apps/RSEM/install_1.3.0.sh
rename to apps/rsem/install_1.3.0.sh
diff --git a/apps/RSEM/install_1.3.1.sh b/apps/rsem/install_1.3.1.sh
similarity index 100%
rename from apps/RSEM/install_1.3.1.sh
rename to apps/rsem/install_1.3.1.sh
diff --git a/apps/Salmon/install_0.8.2.sh b/apps/salmon/install_0.8.2.sh
similarity index 100%
rename from apps/Salmon/install_0.8.2.sh
rename to apps/salmon/install_0.8.2.sh
diff --git a/apps/SAMtools/install_1.5.sh b/apps/samtools/install_1.5.sh
similarity index 100%
rename from apps/SAMtools/install_1.5.sh
rename to apps/samtools/install_1.5.sh
diff --git a/apps/SAMtools/install_1.7.sh b/apps/samtools/install_1.7.sh
similarity index 100%
rename from apps/SAMtools/install_1.7.sh
rename to apps/samtools/install_1.7.sh
diff --git a/apps/SRAtoolkit/install_2.8.2.sh b/apps/sratoolkit/install_2.8.2.sh
similarity index 100%
rename from apps/SRAtoolkit/install_2.8.2.sh
rename to apps/sratoolkit/install_2.8.2.sh
diff --git a/apps/TopHat/install_2.1.1.sh b/apps/tophat/install_2.1.1.sh
similarity index 100%
rename from apps/TopHat/install_2.1.1.sh
rename to apps/tophat/install_2.1.1.sh
diff --git a/apps/Trimmomatic/install_0.36.sh b/apps/trimmomatic/install_0.36.sh
similarity index 100%
rename from apps/Trimmomatic/install_0.36.sh
rename to apps/trimmomatic/install_0.36.sh
diff --git a/apps/UrQt/install_d62c1f8.sh b/apps/urqt/install_d62c1f8.sh
similarity index 100%
rename from apps/UrQt/install_d62c1f8.sh
rename to apps/urqt/install_d62c1f8.sh
diff --git a/modulefiles/BCFtools/1.7.lua b/modulefiles/bcftools/1.7.lua
similarity index 100%
rename from modulefiles/BCFtools/1.7.lua
rename to modulefiles/bcftools/1.7.lua
diff --git a/modulefiles/BEDtools/2.25.0.lua b/modulefiles/bedtools/2.25.0.lua
similarity index 100%
rename from modulefiles/BEDtools/2.25.0.lua
rename to modulefiles/bedtools/2.25.0.lua
diff --git a/modulefiles/Bowtie2/2.3.2.lua b/modulefiles/bowtie2/2.3.2.lua
similarity index 100%
rename from modulefiles/Bowtie2/2.3.2.lua
rename to modulefiles/bowtie2/2.3.2.lua
diff --git a/modulefiles/Bowtie2/2.3.4.1.lua b/modulefiles/bowtie2/2.3.4.1.lua
similarity index 100%
rename from modulefiles/Bowtie2/2.3.4.1.lua
rename to modulefiles/bowtie2/2.3.4.1.lua
diff --git a/modulefiles/CDHIT/4.6.8 b/modulefiles/cdhit/4.6.8
similarity index 100%
rename from modulefiles/CDHIT/4.6.8
rename to modulefiles/cdhit/4.6.8
diff --git a/modulefiles/deepTools/3.0.2.lua b/modulefiles/deeptools/3.0.2.lua
similarity index 100%
rename from modulefiles/deepTools/3.0.2.lua
rename to modulefiles/deeptools/3.0.2.lua
diff --git a/modulefiles/FastQC/0.11.5.lua b/modulefiles/fastqc/0.11.5.lua
similarity index 100%
rename from modulefiles/FastQC/0.11.5.lua
rename to modulefiles/fastqc/0.11.5.lua
diff --git a/modulefiles/GATK/4.0.10.1.lua b/modulefiles/gatk/4.0.10.1.lua
similarity index 100%
rename from modulefiles/GATK/4.0.10.1.lua
rename to modulefiles/gatk/4.0.10.1.lua
diff --git a/modulefiles/GCC/4.9.4.lua b/modulefiles/gcc/4.9.4.lua
similarity index 100%
rename from modulefiles/GCC/4.9.4.lua
rename to modulefiles/gcc/4.9.4.lua
diff --git a/modulefiles/GCC/5.4.0.lua b/modulefiles/gcc/5.4.0.lua
similarity index 100%
rename from modulefiles/GCC/5.4.0.lua
rename to modulefiles/gcc/5.4.0.lua
diff --git a/modulefiles/GCC/6.4.0.lua b/modulefiles/gcc/6.4.0.lua
similarity index 100%
rename from modulefiles/GCC/6.4.0.lua
rename to modulefiles/gcc/6.4.0.lua
diff --git a/modulefiles/GCC/7.2.0.lua b/modulefiles/gcc/7.2.0.lua
similarity index 100%
rename from modulefiles/GCC/7.2.0.lua
rename to modulefiles/gcc/7.2.0.lua
diff --git a/modulefiles/GCC/default b/modulefiles/gcc/default
similarity index 100%
rename from modulefiles/GCC/default
rename to modulefiles/gcc/default
diff --git a/modulefiles/HTSeq/0.8.0.lua b/modulefiles/htseq/0.8.0.lua
similarity index 100%
rename from modulefiles/HTSeq/0.8.0.lua
rename to modulefiles/htseq/0.8.0.lua
diff --git a/modulefiles/HTSeq/0.9.1.lua b/modulefiles/htseq/0.9.1.lua
similarity index 100%
rename from modulefiles/HTSeq/0.9.1.lua
rename to modulefiles/htseq/0.9.1.lua
diff --git a/modulefiles/Java/1.7.0_21.lua b/modulefiles/java/1.7.0_21.lua
similarity index 100%
rename from modulefiles/Java/1.7.0_21.lua
rename to modulefiles/java/1.7.0_21.lua
diff --git a/modulefiles/Java/1.7.0_71.lua b/modulefiles/java/1.7.0_71.lua
similarity index 100%
rename from modulefiles/Java/1.7.0_71.lua
rename to modulefiles/java/1.7.0_71.lua
diff --git a/modulefiles/Java/1.8.0_151.lua b/modulefiles/java/1.8.0_151.lua
similarity index 100%
rename from modulefiles/Java/1.8.0_151.lua
rename to modulefiles/java/1.8.0_151.lua
diff --git a/modulefiles/Kallisto/0.43.1.lua b/modulefiles/kallisto/0.43.1.lua
similarity index 100%
rename from modulefiles/Kallisto/0.43.1.lua
rename to modulefiles/kallisto/0.43.1.lua
diff --git a/modulefiles/Kallisto/0.44.0.lua b/modulefiles/kallisto/0.44.0.lua
similarity index 100%
rename from modulefiles/Kallisto/0.44.0.lua
rename to modulefiles/kallisto/0.44.0.lua
diff --git a/modulefiles/MACS2/2.1.1.20160309.lua b/modulefiles/macs2/2.1.1.20160309.lua
similarity index 100%
rename from modulefiles/MACS2/2.1.1.20160309.lua
rename to modulefiles/macs2/2.1.1.20160309.lua
diff --git a/modulefiles/MultiQC/0.9 b/modulefiles/multiqc/0.9
similarity index 100%
rename from modulefiles/MultiQC/0.9
rename to modulefiles/multiqc/0.9
diff --git a/modulefiles/MultiQC/1.0.lua b/modulefiles/multiqc/1.0.lua
similarity index 100%
rename from modulefiles/MultiQC/1.0.lua
rename to modulefiles/multiqc/1.0.lua
diff --git a/modulefiles/MUSIC/6613c53.lua b/modulefiles/music/6613c53.lua
similarity index 100%
rename from modulefiles/MUSIC/6613c53.lua
rename to modulefiles/music/6613c53.lua
diff --git a/modulefiles/Python/2.7.13.lua b/modulefiles/python/2.7.13.lua
similarity index 100%
rename from modulefiles/Python/2.7.13.lua
rename to modulefiles/python/2.7.13.lua
diff --git a/modulefiles/Python/3.6.1.lua b/modulefiles/python/3.6.1.lua
similarity index 100%
rename from modulefiles/Python/3.6.1.lua
rename to modulefiles/python/3.6.1.lua
diff --git a/modulefiles/R/3.2.4.lua b/modulefiles/r/3.2.4.lua
similarity index 100%
rename from modulefiles/R/3.2.4.lua
rename to modulefiles/r/3.2.4.lua
diff --git a/modulefiles/R/3.4.3.lua b/modulefiles/r/3.4.3.lua
similarity index 100%
rename from modulefiles/R/3.4.3.lua
rename to modulefiles/r/3.4.3.lua
diff --git a/modulefiles/RSEM/1.3.0.lua b/modulefiles/rsem/1.3.0.lua
similarity index 100%
rename from modulefiles/RSEM/1.3.0.lua
rename to modulefiles/rsem/1.3.0.lua
diff --git a/modulefiles/RSEM/1.3.1.lua b/modulefiles/rsem/1.3.1.lua
similarity index 100%
rename from modulefiles/RSEM/1.3.1.lua
rename to modulefiles/rsem/1.3.1.lua
diff --git a/modulefiles/Salmon/0.8.2.lua b/modulefiles/salmon/0.8.2.lua
similarity index 100%
rename from modulefiles/Salmon/0.8.2.lua
rename to modulefiles/salmon/0.8.2.lua
diff --git a/modulefiles/SAMtools/1.5.lua b/modulefiles/samtools/1.5.lua
similarity index 100%
rename from modulefiles/SAMtools/1.5.lua
rename to modulefiles/samtools/1.5.lua
diff --git a/modulefiles/SAMtools/1.7.lua b/modulefiles/samtools/1.7.lua
similarity index 100%
rename from modulefiles/SAMtools/1.7.lua
rename to modulefiles/samtools/1.7.lua
diff --git a/modulefiles/SRAtoolkit/2.8.2.lua b/modulefiles/sratoolkit/2.8.2.lua
similarity index 100%
rename from modulefiles/SRAtoolkit/2.8.2.lua
rename to modulefiles/sratoolkit/2.8.2.lua
diff --git a/modulefiles/TopHat/2.1.1.lua b/modulefiles/tophat/2.1.1.lua
similarity index 100%
rename from modulefiles/TopHat/2.1.1.lua
rename to modulefiles/tophat/2.1.1.lua
diff --git a/modulefiles/Trimmomatic/0.37.lua b/modulefiles/trimmomatic/0.37.lua
similarity index 100%
rename from modulefiles/Trimmomatic/0.37.lua
rename to modulefiles/trimmomatic/0.37.lua
diff --git a/modulefiles/UrQt/d62c1f8.lua b/modulefiles/urqt/d62c1f8.lua
similarity index 100%
rename from modulefiles/UrQt/d62c1f8.lua
rename to modulefiles/urqt/d62c1f8.lua
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