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mmassaviol
WApps
Commits
5192ea01
Commit
5192ea01
authored
Dec 11, 2019
by
khalid
Browse files
Merge branch 'master' of
https://gitlab.mbb.univ-montp2.fr/mmassaviol/wapps
parents
d9885ab2
f687d721
Changes
13
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Genome_Profile/Dockerfile
View file @
5192ea01
...
...
@@ -19,16 +19,18 @@ RUN cd /opt/biotools \
ENV
LANG en_US.UTF-8
ENV
LANGUAGE en_US:en
ENV
LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV
LC_ALL en_US.UTF-8
RUN
mkdir
-p
/share/apps/bin
\
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE
3838
...
...
Interop_report/Dockerfile
View file @
5192ea01
...
...
@@ -13,16 +13,18 @@ RUN apt install -y gnuplot
ENV
LANG en_US.UTF-8
ENV
LANGUAGE en_US:en
ENV
LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV
LC_ALL en_US.UTF-8
RUN
mkdir
-p
/share/apps/bin
\
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE
3838
...
...
Long_Read_Assembly/Dockerfile
View file @
5192ea01
...
...
@@ -59,16 +59,18 @@ RUN cd /opt/biotools \
ENV
LANG en_US.UTF-8
ENV
LANGUAGE en_US:en
ENV
LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV
LC_ALL en_US.UTF-8
RUN
mkdir
-p
/share/apps/bin
\
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE
3838
...
...
Metabarcoding/Dockerfile
View file @
5192ea01
...
...
@@ -28,16 +28,18 @@ RUN cd /opt/biotools \
ENV
LANG en_US.UTF-8
ENV
LANGUAGE en_US:en
ENV
LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV
LC_ALL en_US.UTF-8
RUN
mkdir
-p
/share/apps/bin
\
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE
3838
...
...
MitoZ/Dockerfile
View file @
5192ea01
...
...
@@ -61,16 +61,18 @@ RUN cd /opt/biotools \
ENV
LANG en_US.UTF-8
ENV
LANGUAGE en_US:en
ENV
LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV
LC_ALL en_US.UTF-8
RUN
mkdir
-p
/share/apps/bin
\
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE
3838
...
...
Mito_Assembler_Megahit/Dockerfile
View file @
5192ea01
...
...
@@ -30,7 +30,8 @@ RUN apt-get install -y circos \
&&
cd
/opt/biotools
&&
wget http://circos.ca/distribution/circos-current.tgz
\
&&
tar
-xzf
circos-current.tgz
\
&&
rm
-rf
circos-current.tgz
\
&&
mv
circos
*
circos_current
&&
mv
circos
*
circos_current
\
&&
sed
-i
's/max_points_per_track.*/max_points_per_track = 40000/'
/opt/biotools/circos_current/etc/housekeeping.conf
RUN
cd
/opt/biotools
\
&&
wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2
\
...
...
@@ -71,16 +72,18 @@ RUN cd /opt/biotools \
ENV
LANG en_US.UTF-8
ENV
LANGUAGE en_US:en
ENV
LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV
LC_ALL en_US.UTF-8
RUN
mkdir
-p
/share/apps/bin
\
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE
3838
...
...
Mito_Assembler_Megahit/files/Snakefile
View file @
5192ea01
...
...
@@ -287,7 +287,7 @@ rule mitoz_annotate_SE:
clade = config["clade"],
sample_suffix = config["sample_suffix"]
shell:
"cat {input.read} > reads_R1.{params.sample_suffix} "
"cat {input.read} >
{params.results_dir}/
reads_R1.{params.sample_suffix} "
"&& /opt/biotools/release_MitoZ_v2.4-alpha/MitoZ.py annotate "
"--fastq1 reads_R1.{params.sample_suffix} "
#"--fq_size 0 "
...
...
@@ -319,7 +319,7 @@ rule mitoz_annotate_SE:
"else \n"
" mv circos.png circos_mqc.png \n"
"fi \n"
"rm reads_R1.{params.sample_suffix} "
"rm
{params.results_dir}/
reads_R1.{params.sample_suffix} "
rule mitoz_annotate_PE:
input:
...
...
@@ -338,8 +338,8 @@ rule mitoz_annotate_PE:
clade = config["clade"],
sample_suffix = config["sample_suffix"]
shell:
"cat {input.read} > reads_R1.{params.sample_suffix} "
"&& cat {input.read2} > reads_R2.{params.sample_suffix} "
"cat {input.read} >
{params.results_dir}/
reads_R1.{params.sample_suffix} "
"&& cat {input.read2} >
{params.results_dir}/
reads_R2.{params.sample_suffix} "
"&& /opt/biotools/release_MitoZ_v2.4-alpha/MitoZ.py annotate "
"--fastq1 reads_R1.{params.sample_suffix} "
"--fastq2 reads_R2.{params.sample_suffix} "
...
...
@@ -372,8 +372,8 @@ rule mitoz_annotate_PE:
"else \n"
" mv circos.png circos_mqc.png \n"
"fi \n"
"rm reads_R1.{params.sample_suffix} "
"&& rm reads_R2.{params.sample_suffix} "
"rm
{params.results_dir}/
reads_R1.{params.sample_suffix} "
"&& rm
{params.results_dir}/
reads_R2.{params.sample_suffix} "
ruleorder: mitoz_annotate_PE > mitoz_annotate_SE
...
...
Mito_Assembler_Megahit/files/singularity.def
View file @
5192ea01
...
...
@@ -110,6 +110,7 @@ singularity run --app appName this_container.sif
rm -rf circos-current.tgz
mv circos* circos_current
echo 'export PATH="/opt/biotools/circos_current/bin:$PATH"' >>$SINGULARITY_ENVIRONMENT
sed -i 's/max_points_per_track.*/max_points_per_track = 40000/' /opt/biotools/circos_current/etc/housekeeping.conf
cd /opt/biotools
wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2
...
...
RADseq_denovo/Dockerfile
View file @
5192ea01
...
...
@@ -21,16 +21,18 @@ RUN Rscript -e 'BiocManager::install("SNPRelate", version = "3.8",Ncpus=8, clean
ENV
LANG en_US.UTF-8
ENV
LANGUAGE en_US:en
ENV
LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV
LC_ALL en_US.UTF-8
RUN
mkdir
-p
/share/apps/bin
\
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE
3838
...
...
RADseq_ref/Dockerfile
View file @
5192ea01
...
...
@@ -44,16 +44,18 @@ RUN Rscript -e 'BiocManager::install("SNPRelate", version = "3.8",Ncpus=8, clean
ENV
LANG en_US.UTF-8
ENV
LANGUAGE en_US:en
ENV
LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV
LC_ALL en_US.UTF-8
RUN
mkdir
-p
/share/apps/bin
\
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE
3838
...
...
RNAseq/Dockerfile
View file @
5192ea01
...
...
@@ -44,16 +44,18 @@ RUN Rscript -e 'BiocManager::install("BiocParallel", version = "3.8",Ncpus=8, cl
ENV
LANG en_US.UTF-8
ENV
LANGUAGE en_US:en
ENV
LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV
LC_ALL en_US.UTF-8
RUN
mkdir
-p
/share/apps/bin
\
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE
3838
...
...
Variant_calling/Dockerfile
View file @
5192ea01
...
...
@@ -60,16 +60,18 @@ RUN apt install -y tabix
ENV
LANG en_US.UTF-8
ENV
LANGUAGE en_US:en
ENV
LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV
LC_ALL en_US.UTF-8
RUN
mkdir
-p
/share/apps/bin
\
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE
3838
...
...
Virus_Assembler_Megahit/Dockerfile
View file @
5192ea01
...
...
@@ -45,16 +45,18 @@ RUN cd /opt/biotools \
ENV
LANG en_US.UTF-8
ENV
LANGUAGE en_US:en
ENV
LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin
&& mkdir /share/apps/lib
&& mkdir /share/apps/gridengine
&& mkdir /share/bio
&& mkdir -p /opt/gridengine
&& mkdir -p /export/scrach
&& mkdir -p /usr/lib64
&& ln -s /bin/bash /bin/mbb_bash
&& ln -s /bin/bash /bin/isem_bash
&& /usr/sbin/groupadd --system --gid 400 sge
ENV
LC_ALL en_US.UTF-8
RUN
mkdir
-p
/share/apps/bin
\
&& mkdir /share/apps/lib \
&& mkdir /share/apps/gridengine \
&& mkdir /share/bio \
&& mkdir -p /opt/gridengine \
&& mkdir -p /export/scrach \
&& mkdir -p /usr/lib64 \
&& ln -s /bin/bash /bin/mbb_bash \
&& ln -s /bin/bash /bin/isem_bash \
&& /usr/sbin/groupadd --system --gid 400 sge \
&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
EXPOSE
3838
...
...
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