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author
Antony Le Béchec
committed
V20210412
1 parent f2834d8 commit 34e3ef8

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-1016
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‎.env‎

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@@ -24,7 +24,7 @@ DOCKER_COMPOSE_ENV=.env
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# Docker HOWARD image including HOWARD tool and configuration
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# This image will be build if needed (using Docker HOWARD context)
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#DOCKER_HOWARD_IMAGE=howard:latest
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DOCKER_HOWARD_IMAGE=howard:0.9.15.3
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DOCKER_HOWARD_IMAGE=howard:0.9.15.4
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### DOCKER HOWARD CONTEXT
@@ -58,9 +58,58 @@ DOCKER_HOWARD_CLI_SLEEP=600
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### FOLDERS
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DOCKER_HOWARD_CLI_FOLDER_HOST_DATABASES=~${HOME}/STARK/databases/annovar/current
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DOCKER_HOWARD_CLI_FOLDER_INNER_DATABASES=/databases/annovar
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# HOST
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DOCKER_HOWARD_CLI_FOLDER_HOST_DATABASES=${HOME}/HOWARD/databases
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DOCKER_HOWARD_CLI_FOLDER_HOST_DATA=${HOME}/HOWARD/data
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# INNER
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DOCKER_HOWARD_CLI_FOLDER_INNER_DATABASES=/databases
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DOCKER_HOWARD_CLI_FOLDER_INNER_DATA=/data
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# SERVICE SETUP
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################
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### DOCKER HOWARD SERVICE CLI IMAGE
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# Docker HOWARD service to build images if necessary. Usually on a git repository or locally
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DOCKER_HOWARD_SETUP_IMAGE=${DOCKER_HOWARD_IMAGE}
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### DOCKER HOWARD SERVICE CLI CONTAINER NAME
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DOCKER_HOWARD_SETUP_CONTAINER_NAME=HOWARD-setup
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### Databases folders
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DOCKER_HOWARD_SETUP_ANNOVAR_DATABASES=${DOCKER_HOWARD_CLI_FOLDER_INNER_DATABASES}/annovar/current
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DOCKER_HOWARD_SETUP_SNPEFF_DATABASES=${DOCKER_HOWARD_CLI_FOLDER_INNER_DATABASES}/snpeff/current
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### Databases annotation options
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# Assembly
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DOCKER_HOWARD_SETUP_ASSEMBLY=hg19
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# Annotation
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# Use "ALL" to annotate, test and download all available databases (defined in the HOWARD configuration annotation file)
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# Use "core" to annotate, test and download only core databases (symbol, outcom, location, hgvs, dbSNP... see HOWARD doc)
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# Use "<annovar_code>" to annotate, test and download a custom annovar database (see code on annovar website)
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# Use "symbol" to annotate, test and download only symbol annotation
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# Use "snpeff" to annotate, test and download snpEff databases
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DOCKER_HOWARD_SETUP_ANNOTATION="core,CLINVAR,COSMIC,snpeff"
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### setup command
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# Annotation trough HOWARD annotation
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# All daabases can be downloaded independently, see ANNOVAR and snpEff doc
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# This simple command actually does not work for snpEff 5.0e (due to snpEff bug)
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#DOCKER_HOWARD_SETUP_CONTAINER_COMMAND='-c "mkdir -p ${DOCKER_HOWARD_SETUP_ANNOVAR_DATABASES} ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES} && HOWARD --input=/tool/docs/example.vcf --output=/tmp/example.howard.vcf.gz --annotation=symbol,snpeff --calculation=BARCODE --prioritization=default --translation=VCF --compress=5 --index --verbose --threads=1 && bcftools view /tmp/example.howard.vcf.gz && echo \"# HOWARD setup and test checked!\""'
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# This command actually does not work for snpEff 5.0e (due to snpEff bug)
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#DOCKER_HOWARD_SETUP_CONTAINER_COMMAND='-c "mkdir -p ${DOCKER_HOWARD_SETUP_ANNOVAR_DATABASES} ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES} && if [ ! -d ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/${DOCKER_HOWARD_SETUP_ASSEMBLY} ]; then $JAVA -jar -Xmx4g -jar $SNPEFF download ${DOCKER_HOWARD_SETUP_ASSEMBLY}; fi && HOWARD --input=/tool/docs/example.vcf --output=/tmp/example.howard.vcf.gz --annotation=symbol,snpeff --calculation=BARCODE --prioritization=default --translation=VCF --compress=5 --index --verbose --threads=1 && bcftools view /tmp/example.howard.vcf.gz && echo \"# HOWARD setup and test checked!\""'
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# This command is more manual, but works (only for snpEff 5.0 and the indicated assembly)
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DOCKER_HOWARD_SETUP_CONTAINER_COMMAND='-c "mkdir -p ${DOCKER_HOWARD_SETUP_ANNOVAR_DATABASES} ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES} && if [ ! -d ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/${DOCKER_HOWARD_SETUP_ASSEMBLY} ]; then wget --progress=bar -O ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/snpEff_v5_0_${DOCKER_HOWARD_SETUP_ASSEMBLY}.zip https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_${DOCKER_HOWARD_SETUP_ASSEMBLY}.zip ; unzip ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/snpEff_v5_0_${DOCKER_HOWARD_SETUP_ASSEMBLY}.zip -d ${DOCKER_HOWARD_SETUP_SNPEFF_DATABASES}/; fi && HOWARD --input=/tool/docs/example.vcf --output=/tmp/example.howard.vcf.gz --annotation=${DOCKER_HOWARD_SETUP_ANNOTATION} --calculation=BARCODE --prioritization=default --translation=VCF --compress=5 --index --verbose --threads=1 && bcftools view /tmp/example.howard.vcf.gz && echo \"# HOWARD setup and test checked!\""'
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‎Dockerfile‎

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@@ -1,8 +1,8 @@
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##############################################################
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# Dockerfile Version: 1.4.2
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# Dockerfile Version: 1.5
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# Software: HOWARD
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# Software Version: 0.9.15.2
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# Software Version: 0.9.15.4
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# Software Website: https://gitlab.bioinfo-diag.fr/Strasbourg/HOWARD
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# Licence: GNU Affero General Public License (AGPL)
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# Description: HOWARD
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FROM centos:7
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LABEL Software="HOWARD" \
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Version="0.9.15.2" \
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Version="0.9.15.4" \
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Website="https://gitlab.bioinfo-diag.fr/Strasbourg/HOWARD" \
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Description="HOWARD" \
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License="GNU Affero General Public License (AGPL)" \
@@ -65,7 +65,7 @@ ENV DATA=/data
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ENV TOOL=/tool
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ENV DATABASES=/databases
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ENV YUM_INSTALL="gcc bc make wget perl-Switch perl-Digest-MD5 perl-Data-Dumper which zlib-devel zlib zlib2-devel zlib2 bzip2-devel bzip2 lzma-devel lzma xz-devel xz ncurses-devel unzip curl-devel"
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ENV YUM_REMOVE="zlib-devel bzip2-devel xz-devel ncurses-devel unzip gcc"
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ENV YUM_REMOVE="zlib-devel bzip2-devel xz-devel ncurses-devel gcc"
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@@ -87,7 +87,7 @@ RUN yum install -y $YUM_INSTALL ;
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##########
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ENV TOOL_NAME=htslib
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ENV TOOL_VERSION=1.11
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ENV TOOL_VERSION=1.12
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ENV TARBALL_LOCATION=https://github.com/samtools/$TOOL_NAME/releases/download/$TOOL_VERSION/
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ENV TARBALL=$TOOL_NAME-$TOOL_VERSION.tar.bz2
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ENV DEST=$TOOLS/$TOOL_NAME/$TOOL_VERSION
@@ -100,6 +100,7 @@ RUN wget $TARBALL_LOCATION/$TARBALL && \
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cd $TOOL_NAME-$TOOL_VERSION && \
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make -j $THREADS prefix=$TOOLS/$TOOL_NAME/$TOOL_VERSION install && \
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cd ../ && \
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ln -s $TOOL_VERSION $TOOLS/$TOOL_NAME/current && \
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rm -rf $TOOL_NAME-$TOOL_VERSION
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############
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ENV TOOL_NAME=bcftools
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ENV TOOL_VERSION=1.11
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ENV TOOL_VERSION=1.12
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ENV TARBALL_LOCATION=https://github.com/samtools/$TOOL_NAME/releases/download/$TOOL_VERSION/
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ENV TARBALL=$TOOL_NAME-$TOOL_VERSION.tar.bz2
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ENV DEST=$TOOLS/$TOOL_NAME/$TOOL_VERSION
@@ -122,6 +123,7 @@ RUN wget $TARBALL_LOCATION/$TARBALL && \
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cd $TOOL_NAME-$TOOL_VERSION && \
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make -j $THREADS prefix=$TOOLS/$TOOL_NAME/$TOOL_VERSION install && \
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cd ../ && \
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ln -s $TOOL_VERSION $TOOLS/$TOOL_NAME/current && \
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rm -rf $TOOL_NAME-$TOOL_VERSION
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RUN yum install -y java-$TOOL_VERSION && \
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mkdir -p $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin && \
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ln -s /usr/bin/java $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/java && \
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ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current ;
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ln -s $TOOL_VERSION $TOOLS/$TOOL_NAME/current ;
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ENV DATABASES=/databases
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ENV TOOL_NAME=snpeff
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ENV TOOL_VERSION=4.3t
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ENV TOOL_VERSION_FOR_FILE=4_3t
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ENV TARBALL_LOCATION=https://sourceforge.net/projects/snpeff/files
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ENV TARBALL="snpEff_v"$TOOL_VERSION_FOR_FILE"_core.zip"
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ENV TOOL_VERSION=5.0e
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ENV TARBALL="snpEff_latest_core.zip"
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ENV TARBALL_LOCATION=https://snpeff.blob.core.windows.net/versions
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ENV TARBALL_FOLDER=snpeff_folder
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ENV TOOL_DATABASE_FOLDER=$DATABASES/snpeff/$TOOL_VERSION
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ENV TOOL_DATABASE_FOLDER=$DATABASES/snpeff/current
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ENV DEST=$TOOLS/$TOOL_NAME/$TOOL_VERSION
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ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
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ENV SNPEFF_DATABASES=$TOOL_DATABASE_FOLDER
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# INSTALL
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mkdir -p $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/ && \
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cp $TARBALL_FOLDER/*/*jar $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/ -R && \
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cp $TARBALL_FOLDER/*/*.config $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/ -R && \
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ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current && \
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ln -s $TOOL_VERSION $TOOLS/$TOOL_NAME/current && \
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mkdir -p $TOOL_DATABASE_FOLDER && \
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ln -s $TOOL_DATABASE_FOLDER $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/data ;
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ENV TARBALL_LOCATION=http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP
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ENV TARBALL=annovar.latest.tar.gz
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ENV TARBALL_FOLDER=$TOOL_NAME
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ENV TOOL_DATABASE_FOLDER=$DATABASES/annovar
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ENV TOOL_DATABASE_FOLDER=$DATABASES/annovar/current
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ENV DEST=$TOOLS/$TOOL_NAME/$TOOL_VERSION
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ENV PATH=$TOOLS/$TOOL_NAME/$TOOL_VERSION/bin:$PATH
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ENV ANNOVAR_DATABASES=$TOOL_DATABASE_FOLDER
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# http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz
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cp *.pl $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/ -R && \
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cd ../ && \
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rm -rf $TARBALL_FOLDER && \
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ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current && \
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ln -s $TOOL_VERSION $TOOLS/$TOOL_NAME/current && \
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mkdir -p $TOOL_DATABASE_FOLDER && \
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ln -s $TOOL_DATABASE_FOLDER $TOOLS/$TOOL_NAME/$TOOL_VERSION/bin/databases ;
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ENV DATABASES=/databases
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ENV TOOL_NAME=howard
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ENV TOOL_VERSION=0.9.15.2
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ENV TOOL_VERSION=0.9.15.4
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ENV TARBALL_LOCATION=https://gitlab.bioinfo-diag.fr/Strasbourg/HOWARD/repository/$TOOL_VERSION
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ENV TARBALL=archive.tar.gz
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ENV TARBALL_FOLDER=archive
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RUN ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current && \
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chmod 0775 $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current -R && \
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mkdir -p $DATABASES && \
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ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION $TOOLS/$TOOL_NAME/current && \
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ln -s $TOOL_VERSION $TOOLS/$TOOL_NAME/current && \
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ln -s $TOOLS/$TOOL_NAME/$TOOL_VERSION/ /tool ;
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‎LICENSE‎

100644100755
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