From 96a219ea0b3fd278a28c942d5fd3cf25f800c693 Mon Sep 17 00:00:00 2001 From: Johannes Griss Date: Wed, 31 Oct 2018 19:17:11 +0000 Subject: [PATCH 1/5] spectra-cluster-cli v1.1.2 --- spectra-cluster-cli/v1.1.2/Dockerfile | 29 +++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 spectra-cluster-cli/v1.1.2/Dockerfile diff --git a/spectra-cluster-cli/v1.1.2/Dockerfile b/spectra-cluster-cli/v1.1.2/Dockerfile new file mode 100644 index 000000000..4c89ad3f1 --- /dev/null +++ b/spectra-cluster-cli/v1.1.2/Dockerfile @@ -0,0 +1,29 @@ +################## BASE IMAGE ###################### +FROM biocontainers/biocontainers:latest + +################## METADATA ###################### +LABEL base_image="biocontainers:latest" +LABEL version="1" +LABEL software="spectra-cluster-cli" +LABEL software.version="v1.1.2" +LABEL about.summary="PRIDE Cluster algorithm to cluster heterogeneous mass spectra" +LABEL about.home="https://github.com/spectra-cluster/spectra-cluster-cli" +LABEL about.documentation="https://github.com/spectra-cluster/spectra-cluster-cli" +LABEL about.license_file="https://github.com/spectra-cluster/spectra-cluster-cli/LICENSE" +LABEL about.license="SPDX:Apache-2.0" +LABEL about.tags="Proteomics" + +################## MAINTAINER ###################### +MAINTAINER Johannes Griss + +RUN VERSION=1.1.2 && \ + ZIP=spectra-cluster-cli-${VERSION}-bin.zip && \ + wget https://github.com/spectra-cluster/spectra-cluster-cli/releases/download/spectra-cluster-cli-${VERSION}/$ZIP -O /tmp/$ZIP && \ + unzip /tmp/$ZIP -d /home/biodocker/bin/ && \ + rm /tmp/$ZIP && \ + bash -c 'echo -e "#!/bin/bash\njava -jar /home/biodocker/bin/spectra-cluster-cli-1.1.2.jar $@" > /home/biodocker/bin/spectra-cluster-cli' && \ + chmod +x /home/biodocker/bin/spectra-cluster-cli + +ENV PATH /home/biodocker/bin/spectra-cluster-cli:$PATH + +WORKDIR /data/ From cc4112038b82a011cc6f6e28841db11500106c79 Mon Sep 17 00:00:00 2001 From: Johannes Griss Date: Thu, 1 Nov 2018 09:23:53 +0000 Subject: [PATCH 2/5] Fixed a bug in the Dockerfile which prevented parametes to be passed on. --- spectra-cluster-cli/v1.1.2/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/spectra-cluster-cli/v1.1.2/Dockerfile b/spectra-cluster-cli/v1.1.2/Dockerfile index 4c89ad3f1..3f37d24e7 100644 --- a/spectra-cluster-cli/v1.1.2/Dockerfile +++ b/spectra-cluster-cli/v1.1.2/Dockerfile @@ -21,7 +21,7 @@ RUN VERSION=1.1.2 && \ wget https://github.com/spectra-cluster/spectra-cluster-cli/releases/download/spectra-cluster-cli-${VERSION}/$ZIP -O /tmp/$ZIP && \ unzip /tmp/$ZIP -d /home/biodocker/bin/ && \ rm /tmp/$ZIP && \ - bash -c 'echo -e "#!/bin/bash\njava -jar /home/biodocker/bin/spectra-cluster-cli-1.1.2.jar $@" > /home/biodocker/bin/spectra-cluster-cli' && \ + echo -e '#!/bin/bash\njava -jar /home/biodocker/bin/spectra-cluster-cli-1.1.2.jar $@' > /home/biodocker/bin/spectra-cluster-cli && \ chmod +x /home/biodocker/bin/spectra-cluster-cli ENV PATH /home/biodocker/bin/spectra-cluster-cli:$PATH From 9cc521e831926505ebba5487ce3c87004af05ea3 Mon Sep 17 00:00:00 2001 From: Johannes Griss Date: Tue, 8 Jan 2019 09:56:06 +0000 Subject: [PATCH 3/5] Added Dockerfile for X!Tandem 17-02-01-4 --- tandem/17-02-01-4/Dockerfile | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 tandem/17-02-01-4/Dockerfile diff --git a/tandem/17-02-01-4/Dockerfile b/tandem/17-02-01-4/Dockerfile new file mode 100644 index 000000000..b2bac8b76 --- /dev/null +++ b/tandem/17-02-01-4/Dockerfile @@ -0,0 +1,35 @@ + +################## BASE IMAGE ###################### +FROM biocontainers/biocontainers:v1.0.0_cv4 + +################## METADATA ###################### +LABEL base_image="biocontainers:v1.0.0_cv4" +LABEL version="4" +LABEL software="X!Tandem" +LABEL software.version="17-02-01-4" +LABEL about.summary="software that can match tandem mass spectra with peptide sequences" +LABEL about.home="http://www.thegpm.org/tandem/" +LABEL about.documentation="http://www.thegpm.org/tandem/" +LABEL about.license_file="http://www.thegpm.org/tandem/" +LABEL about.license="SPDX:Artistic-2.0" +LABEL about.tags="Proteomics" +LABEL extra.identifiers.biotools="xtandem" + +################## MAINTAINER ###################### +MAINTAINER Johannes Griss + +RUN ZIP=tandem-linux-17-02-01-4.zip && \ + wget "ftp://ftp.thegpm.org/projects/tandem/source/${ZIP}" -O /tmp/$ZIP && \ + # wget https://github.com/BioDocker/software-archive/releases/download/X!Tandem/$ZIP -O /tmp/$ZIP && \ + unzip /tmp/$ZIP -d /home/biodocker/bin/ && \ + chmod 755 /home/biodocker/bin/tandem-linux-17-02-01-4/bin/tandem.exe && \ + rm /tmp/$ZIP + +RUN bash -c 'echo -e "#!/bin/bash\n/home/biodocker/bin/tandem-linux-17-02-01-4/bin/tandem.exe \$@"' > /home/biodocker/bin/tandem && \ + chmod 755 /home/biodocker/bin/tandem + +ENV PATH /home/biodocker/bin:$PATH + +USER biodocker + +WORKDIR /data/ From 90f505b33734bf979edcbf5244f8457de3d51e37 Mon Sep 17 00:00:00 2001 From: Johannes Griss Date: Tue, 8 Jan 2019 11:44:19 +0000 Subject: [PATCH 4/5] Makes run_pia.sh executable, otherwise the container fails. --- pia/1.3.8/Dockerfile | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/pia/1.3.8/Dockerfile b/pia/1.3.8/Dockerfile index 68b408ae1..a8decacbd 100644 --- a/pia/1.3.8/Dockerfile +++ b/pia/1.3.8/Dockerfile @@ -24,6 +24,10 @@ ENV ZIP_FILE=pia-1.3.8.zip \ PIA_PATH=/home/biodocker/pia \ PIA_JAR=/home/biodocker/pia/pia-1.3.8.jar +COPY ./runpia.sh $USER_HOME/bin/ + +RUN chmod +x $USER_HOME/bin/runpia.sh + USER biodocker RUN set -x \ @@ -31,8 +35,6 @@ RUN set -x \ && unzip $USER_HOME/$ZIP_FILE -d $PIA_PATH \ && rm $USER_HOME/$ZIP_FILE -COPY ./runpia.sh $USER_HOME/bin/ - WORKDIR /data/ ENTRYPOINT ["runpia.sh"] From 2931c9f647c862673052d78103e519ff3feb86ab Mon Sep 17 00:00:00 2001 From: Johannes Griss Date: Tue, 8 Jan 2019 15:14:07 +0000 Subject: [PATCH 5/5] Fixed software name for new X!Tandem version. --- tandem/17-02-01-4/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tandem/17-02-01-4/Dockerfile b/tandem/17-02-01-4/Dockerfile index b2bac8b76..1935744af 100644 --- a/tandem/17-02-01-4/Dockerfile +++ b/tandem/17-02-01-4/Dockerfile @@ -5,7 +5,7 @@ FROM biocontainers/biocontainers:v1.0.0_cv4 ################## METADATA ###################### LABEL base_image="biocontainers:v1.0.0_cv4" LABEL version="4" -LABEL software="X!Tandem" +LABEL software="tandem" LABEL software.version="17-02-01-4" LABEL about.summary="software that can match tandem mass spectra with peptide sequences" LABEL about.home="http://www.thegpm.org/tandem/"