From e82c23907783ecf6ff3184e757cb9a528c3eeac0 Mon Sep 17 00:00:00 2001 From: avani-bhojwani Date: Sat, 10 Jun 2023 22:01:52 +1000 Subject: [PATCH 1/6] added Dockerfile for evigene --- evidential-gene/1.0.0/Dockerfile | 37 ++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 evidential-gene/1.0.0/Dockerfile diff --git a/evidential-gene/1.0.0/Dockerfile b/evidential-gene/1.0.0/Dockerfile new file mode 100644 index 00000000..29bc24b3 --- /dev/null +++ b/evidential-gene/1.0.0/Dockerfile @@ -0,0 +1,37 @@ +################## BASE IMAGE ###################### +FROM biocontainers/biocontainers:v1.0.0_cv4 + +################## METADATA ###################### +LABEL base_image="biocontainers:v1.0.0_cv4" +LABEL version="1" +LABEL software="EvidentialGene" +LABEL software.version="22jan14" +LABEL about.summary="EvidentialGene is a genome informatics project for Evidence Directed Gene Construction for Eukaryotes" +LABEL about.home="http://arthropods.eugenes.org/EvidentialGene/evigene/" +LABEL about.documentation="http://arthropods.eugenes.org/EvidentialGene/evigene/docs/" +LABEL about.license_file="http://arthropods.eugenes.org/about/about-EvidentialGene/" +LABEL about.tags="Genomics, Transcriptomics" + +################## MAINTAINER ###################### +MAINTAINER Avani Bhojwani + +################## INSTALLATION ###################### + +USER 0 + +RUN apt-get update && apt-get upgrade -y && \ + apt-get install -y perl cpanminus exonerate cd-hit ncbi-blast+ && \ + wget -O EvidentialGene.tar http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene22jan14.tar && \ + tar -xvf EvidentialGene.tar && rm EvidentialGene.tar && \ + chmod +x evigene/scripts/*.pl && \ + mv evigene /home/biodocker/bin/ && \ + ln -s /usr/bin/cdhit /usr/bin/cd-hit && \ + ln -s /usr/bin/cdhit-est /usr/bin/cd-hit-est && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + +ENV PATH="/home/biodocker/bin/evigene/scripts:/home/biodocker/bin/evigene/scripts/genoasm:/home/biodocker/bin/evigene/scripts/genes:/home/biodocker/bin/evigene/scripts/prot:/home/biodocker/bin/evigene/scripts/genes/evgpipe_scriptwork:/home/biodocker/bin/evigene/scripts/rnaseq:/home/biodocker/bin/evigene/scripts/omcl:/home/biodocker/bin/evigene/scripts/grid:/home/biodocker/bin/evigene/scripts/ests:${PATH}" + +USER biodocker + +WORKDIR /data/ From a634bc85be2ba7fb84f28810cfe7061e6e31e382 Mon Sep 17 00:00:00 2001 From: avani-bhojwani Date: Sun, 11 Jun 2023 08:36:31 +1000 Subject: [PATCH 2/6] renamed directory --- {evidential-gene/1.0.0 => EvidentialGene/22jan14}/Dockerfile | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {evidential-gene/1.0.0 => EvidentialGene/22jan14}/Dockerfile (100%) diff --git a/evidential-gene/1.0.0/Dockerfile b/EvidentialGene/22jan14/Dockerfile similarity index 100% rename from evidential-gene/1.0.0/Dockerfile rename to EvidentialGene/22jan14/Dockerfile From ea8a71dc6256547d8058e1b353af374a674e8c16 Mon Sep 17 00:00:00 2001 From: avani-bhojwani Date: Sun, 11 Jun 2023 18:06:11 +1000 Subject: [PATCH 3/6] changed name to lowercase --- {EvidentialGene => evidential-gene}/22jan14/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename {EvidentialGene => evidential-gene}/22jan14/Dockerfile (98%) diff --git a/EvidentialGene/22jan14/Dockerfile b/evidential-gene/22jan14/Dockerfile similarity index 98% rename from EvidentialGene/22jan14/Dockerfile rename to evidential-gene/22jan14/Dockerfile index 29bc24b3..dd3f0d33 100644 --- a/EvidentialGene/22jan14/Dockerfile +++ b/evidential-gene/22jan14/Dockerfile @@ -4,7 +4,7 @@ FROM biocontainers/biocontainers:v1.0.0_cv4 ################## METADATA ###################### LABEL base_image="biocontainers:v1.0.0_cv4" LABEL version="1" -LABEL software="EvidentialGene" +LABEL software="evidential-gene" LABEL software.version="22jan14" LABEL about.summary="EvidentialGene is a genome informatics project for Evidence Directed Gene Construction for Eukaryotes" LABEL about.home="http://arthropods.eugenes.org/EvidentialGene/evigene/" From 769f659e33a427e766a7ec29ce106f2e8cc5af4c Mon Sep 17 00:00:00 2001 From: avani-bhojwani Date: Tue, 10 Oct 2023 19:20:40 +1000 Subject: [PATCH 4/6] add new evigene version and fix path --- evidential-gene/22jan14/Dockerfile | 74 +++++++++++++++--------------- evidential-gene/23jul15/Dockerfile | 37 +++++++++++++++ 2 files changed, 74 insertions(+), 37 deletions(-) create mode 100644 evidential-gene/23jul15/Dockerfile diff --git a/evidential-gene/22jan14/Dockerfile b/evidential-gene/22jan14/Dockerfile index dd3f0d33..8b27f5b1 100644 --- a/evidential-gene/22jan14/Dockerfile +++ b/evidential-gene/22jan14/Dockerfile @@ -1,37 +1,37 @@ -################## BASE IMAGE ###################### -FROM biocontainers/biocontainers:v1.0.0_cv4 - -################## METADATA ###################### -LABEL base_image="biocontainers:v1.0.0_cv4" -LABEL version="1" -LABEL software="evidential-gene" -LABEL software.version="22jan14" -LABEL about.summary="EvidentialGene is a genome informatics project for Evidence Directed Gene Construction for Eukaryotes" -LABEL about.home="http://arthropods.eugenes.org/EvidentialGene/evigene/" -LABEL about.documentation="http://arthropods.eugenes.org/EvidentialGene/evigene/docs/" -LABEL about.license_file="http://arthropods.eugenes.org/about/about-EvidentialGene/" -LABEL about.tags="Genomics, Transcriptomics" - -################## MAINTAINER ###################### -MAINTAINER Avani Bhojwani - -################## INSTALLATION ###################### - -USER 0 - -RUN apt-get update && apt-get upgrade -y && \ - apt-get install -y perl cpanminus exonerate cd-hit ncbi-blast+ && \ - wget -O EvidentialGene.tar http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene22jan14.tar && \ - tar -xvf EvidentialGene.tar && rm EvidentialGene.tar && \ - chmod +x evigene/scripts/*.pl && \ - mv evigene /home/biodocker/bin/ && \ - ln -s /usr/bin/cdhit /usr/bin/cd-hit && \ - ln -s /usr/bin/cdhit-est /usr/bin/cd-hit-est && \ - apt-get clean && \ - rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* - -ENV PATH="/home/biodocker/bin/evigene/scripts:/home/biodocker/bin/evigene/scripts/genoasm:/home/biodocker/bin/evigene/scripts/genes:/home/biodocker/bin/evigene/scripts/prot:/home/biodocker/bin/evigene/scripts/genes/evgpipe_scriptwork:/home/biodocker/bin/evigene/scripts/rnaseq:/home/biodocker/bin/evigene/scripts/omcl:/home/biodocker/bin/evigene/scripts/grid:/home/biodocker/bin/evigene/scripts/ests:${PATH}" - -USER biodocker - -WORKDIR /data/ +################## BASE IMAGE ###################### +FROM biocontainers/biocontainers:v1.0.0_cv4 + +################## METADATA ###################### +LABEL base_image="biocontainers:v1.0.0_cv4" +LABEL version="2" +LABEL software="evidential-gene" +LABEL software.version="22jan14" +LABEL about.summary="EvidentialGene is a genome informatics project for Evidence Directed Gene Construction for Eukaryotes" +LABEL about.home="http://arthropods.eugenes.org/EvidentialGene/evigene/" +LABEL about.documentation="http://arthropods.eugenes.org/EvidentialGene/evigene/docs/" +LABEL about.license_file="http://arthropods.eugenes.org/about/about-EvidentialGene/" +LABEL about.tags="Genomics, Transcriptomics" + +################## MAINTAINER ###################### +MAINTAINER Avani Bhojwani + +################## INSTALLATION ###################### + +USER 0 + +RUN apt-get update && apt-get upgrade -y && \ + apt-get install -y perl cpanminus exonerate cd-hit ncbi-blast+ && \ + wget -O EvidentialGene.tar http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/evigene22jan14.tar && \ + tar -xvf EvidentialGene.tar && rm EvidentialGene.tar && \ + chmod +x evigene/scripts/*.pl && \ + mv evigene /opt/ && \ + ln -s /usr/bin/cdhit /usr/bin/cd-hit && \ + ln -s /usr/bin/cdhit-est /usr/bin/cd-hit-est && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + +ENV PATH="/opt/evigene/scripts:/opt/evigene/scripts/genoasm:/opt/evigene/scripts/genes:/opt/evigene/scripts/prot:/opt/evigene/scripts/genes/evgpipe_scriptwork:/opt/evigene/scripts/rnaseq:/opt/evigene/scripts/omcl:/opt/evigene/scripts/grid:/opt/evigene/scripts/ests:${PATH}" + +USER biodocker + +WORKDIR /data/ diff --git a/evidential-gene/23jul15/Dockerfile b/evidential-gene/23jul15/Dockerfile new file mode 100644 index 00000000..0d45ac14 --- /dev/null +++ b/evidential-gene/23jul15/Dockerfile @@ -0,0 +1,37 @@ +################## BASE IMAGE ###################### +FROM biocontainers/biocontainers:v1.0.0_cv4 + +################## METADATA ###################### +LABEL base_image="biocontainers:v1.0.0_cv4" +LABEL version="1" +LABEL software="evidential-gene" +LABEL software.version="23jul15" +LABEL about.summary="EvidentialGene is a genome informatics project for Evidence Directed Gene Construction for Eukaryotes" +LABEL about.home="http://arthropods.eugenes.org/EvidentialGene/evigene/" +LABEL about.documentation="http://arthropods.eugenes.org/EvidentialGene/evigene/docs/" +LABEL about.license_file="http://arthropods.eugenes.org/about/about-EvidentialGene/" +LABEL about.tags="Genomics, Transcriptomics" + +################## MAINTAINER ###################### +MAINTAINER Avani Bhojwani + +################## INSTALLATION ###################### + +USER 0 + +RUN apt-get update && apt-get upgrade -y && \ + apt-get install -y perl cpanminus exonerate cd-hit ncbi-blast+ && \ + wget -O EvidentialGene.tar http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/evigene23jul15.tar && \ + tar -xvf EvidentialGene.tar && rm EvidentialGene.tar && \ + chmod +x evigene/scripts/*.pl && \ + mv evigene /opt/ && \ + ln -s /usr/bin/cdhit /usr/bin/cd-hit && \ + ln -s /usr/bin/cdhit-est /usr/bin/cd-hit-est && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + +ENV PATH="/opt/evigene/scripts:/opt/evigene/scripts/genoasm:/opt/evigene/scripts/genes:/opt/evigene/scripts/prot:/opt/evigene/scripts/genes/evgpipe_scriptwork:/opt/evigene/scripts/rnaseq:/opt/evigene/scripts/omcl:/opt/evigene/scripts/grid:/opt/evigene/scripts/ests:${PATH}" + +USER biodocker + +WORKDIR /data/ From 7926b7b1886ff707d7c485a9b31821204960c218 Mon Sep 17 00:00:00 2001 From: avani-bhojwani Date: Tue, 10 Oct 2023 20:24:17 +1000 Subject: [PATCH 5/6] deleted new version --- evidential-gene/23jul15/Dockerfile | 37 ------------------------------ 1 file changed, 37 deletions(-) delete mode 100644 evidential-gene/23jul15/Dockerfile diff --git a/evidential-gene/23jul15/Dockerfile b/evidential-gene/23jul15/Dockerfile deleted file mode 100644 index 0d45ac14..00000000 --- a/evidential-gene/23jul15/Dockerfile +++ /dev/null @@ -1,37 +0,0 @@ -################## BASE IMAGE ###################### -FROM biocontainers/biocontainers:v1.0.0_cv4 - -################## METADATA ###################### -LABEL base_image="biocontainers:v1.0.0_cv4" -LABEL version="1" -LABEL software="evidential-gene" -LABEL software.version="23jul15" -LABEL about.summary="EvidentialGene is a genome informatics project for Evidence Directed Gene Construction for Eukaryotes" -LABEL about.home="http://arthropods.eugenes.org/EvidentialGene/evigene/" -LABEL about.documentation="http://arthropods.eugenes.org/EvidentialGene/evigene/docs/" -LABEL about.license_file="http://arthropods.eugenes.org/about/about-EvidentialGene/" -LABEL about.tags="Genomics, Transcriptomics" - -################## MAINTAINER ###################### -MAINTAINER Avani Bhojwani - -################## INSTALLATION ###################### - -USER 0 - -RUN apt-get update && apt-get upgrade -y && \ - apt-get install -y perl cpanminus exonerate cd-hit ncbi-blast+ && \ - wget -O EvidentialGene.tar http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/evigene23jul15.tar && \ - tar -xvf EvidentialGene.tar && rm EvidentialGene.tar && \ - chmod +x evigene/scripts/*.pl && \ - mv evigene /opt/ && \ - ln -s /usr/bin/cdhit /usr/bin/cd-hit && \ - ln -s /usr/bin/cdhit-est /usr/bin/cd-hit-est && \ - apt-get clean && \ - rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* - -ENV PATH="/opt/evigene/scripts:/opt/evigene/scripts/genoasm:/opt/evigene/scripts/genes:/opt/evigene/scripts/prot:/opt/evigene/scripts/genes/evgpipe_scriptwork:/opt/evigene/scripts/rnaseq:/opt/evigene/scripts/omcl:/opt/evigene/scripts/grid:/opt/evigene/scripts/ests:${PATH}" - -USER biodocker - -WORKDIR /data/ From 36bcd4392f167d6fa8292ff2cd1bb459f939576a Mon Sep 17 00:00:00 2001 From: avani-bhojwani Date: Fri, 24 Nov 2023 20:36:03 +1000 Subject: [PATCH 6/6] added new version of EvidentialGene --- evidential-gene/23jul15/Dockerfile | 35 ++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 evidential-gene/23jul15/Dockerfile diff --git a/evidential-gene/23jul15/Dockerfile b/evidential-gene/23jul15/Dockerfile new file mode 100644 index 00000000..a77d74b3 --- /dev/null +++ b/evidential-gene/23jul15/Dockerfile @@ -0,0 +1,35 @@ +################## BASE IMAGE ###################### +FROM biocontainers/biocontainers:v1.2.0_cv2 + +################## METADATA ###################### +LABEL base_image="biocontainers:v1.2.0_cv2" +LABEL version="1" +LABEL software="evidential-gene" +LABEL software.version="23jul15" +LABEL about.summary="EvidentialGene is a genome informatics project for Evidence Directed Gene Construction for Eukaryotes" +LABEL about.home="http://arthropods.eugenes.org/EvidentialGene/evigene/" +LABEL about.documentation="http://arthropods.eugenes.org/EvidentialGene/evigene/docs/" +LABEL about.license_file="http://arthropods.eugenes.org/about/about-EvidentialGene/" +LABEL about.tags="Genomics, Transcriptomics" + +################## MAINTAINER ###################### +MAINTAINER Avani Bhojwani + +################## INSTALLATION ###################### + +USER 0 + +RUN apt-get update && apt-get upgrade -y && \ + apt-get install -y perl cpanminus exonerate cd-hit ncbi-blast+ && \ + wget -O EvidentialGene.tar http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/evigene23jul15.tar && \ + tar -xvf EvidentialGene.tar && rm EvidentialGene.tar && \ + chmod +x evigene/scripts/*.pl && \ + mv evigene /opt/ && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + +ENV PATH="/opt/evigene/scripts:/opt/evigene/scripts/genoasm:/opt/evigene/scripts/genes:/opt/evigene/scripts/prot:/opt/evigene/scripts/genes/evgpipe_scriptwork:/opt/evigene/scripts/rnaseq:/opt/evigene/scripts/omcl:/opt/evigene/scripts/grid:/opt/evigene/scripts/ests:${PATH}" + +USER biodocker + +WORKDIR /data/ \ No newline at end of file