From a524547a706cba1fd6e211bf2b80c7e6f31b8265 Mon Sep 17 00:00:00 2001 From: Amandine PERRIN <amandine.perrin@pasteur.fr> Date: Wed, 2 Sep 2020 21:14:31 +0200 Subject: [PATCH] publish singularity image for version 1.0 --- PanACoTA/__init__.py | 2 +- .../{panacota-singularity.def => Singularity} | 23 +++++++------------ 2 files changed, 9 insertions(+), 16 deletions(-) rename containers/{panacota-singularity.def => Singularity} (97%) diff --git a/PanACoTA/__init__.py b/PanACoTA/__init__.py index 34cb904b..1c86a194 100755 --- a/PanACoTA/__init__.py +++ b/PanACoTA/__init__.py @@ -1,3 +1,3 @@ """PanACoTA""" -__version__ = 20190425 +__version__ = 1.0 diff --git a/containers/panacota-singularity.def b/containers/Singularity similarity index 97% rename from containers/panacota-singularity.def rename to containers/Singularity index 2f2c641a..bbe21147 100644 --- a/containers/panacota-singularity.def +++ b/containers/Singularity @@ -14,10 +14,6 @@ From:python:3.7-stretch # Install packages needed apt-get install -y wget - # apt-get install -y \ - # wget \ - # python3 \ - # python3-pip # Upgrade pip pip3 install --upgrade pip @@ -25,14 +21,6 @@ From:python:3.7-stretch # For manually-installed programs mkdir -p /opt/src - # Update makeblastdb and blastp for prokka - cd /opt/src - wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.1+-x64-linux.tar.gz && \ - tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\ - cp /opt/src/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\ - cp /opt/src/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\ - rm ncbi-blast-2.10.1+-x64-linux.tar.gz - # Install mash cd /opt/src wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar &&\ @@ -40,7 +28,14 @@ From:python:3.7-stretch rm mash-Linux64-v2.2.tar &&\ mv /opt/src/mash-Linux64-v2.2/mash /usr/local/bin &&\ rm -r mash-Linux64-v2.2 - + + # Update makeblastdb and blastp for prokka + cd /opt/src + wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.1+-x64-linux.tar.gz && \ + tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\ + cp /opt/src/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\ + cp /opt/src/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\ + rm ncbi-blast-2.10.1+-x64-linux.tar.gz # Install barrnap cd /opt/src @@ -73,7 +68,6 @@ From:python:3.7-stretch /opt/src/prokka/bin/prokka --setupdb &&\ ln -s /opt/src/prokka/bin/prokka /usr/local/bin - # Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e cd /opt/src wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\ @@ -141,7 +135,6 @@ From:python:3.7-stretch cd /opt/src git clone https://gitlab.pasteur.fr/aperrin/pipeline_annotation.git cd /opt/src/pipeline_annotation - git checkout dev &&\ ./make -- GitLab