From e97910f0d737cddcc17019e75f204754989a121b Mon Sep 17 00:00:00 2001 From: Cyrus-Shahnam Date: Tue, 26 Aug 2025 17:04:14 +0000 Subject: [PATCH] updated to currect public tool 2.1.4 --- Dockerfile | 55 ++++++++++++++++++++++++++++-------------------------- 1 file changed, 29 insertions(+), 26 deletions(-) diff --git a/Dockerfile b/Dockerfile index 7b9910a..1fd475b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM kbase/sdkbase2:python +FROM kbase/sdkpython:3.8.0 MAINTAINER KBase Developer # ----------------------------------------- # In this section, you can install any system dependencies required @@ -9,7 +9,7 @@ MAINTAINER KBase Developer # RUN apt-get update RUN apt-get update --fix-missing -RUN apt-get install -y gcc wget +RUN apt-get install -y gcc wget ca-certificates samtools && rm -rf /var/lib/apt/lists/* # Here we install a python coverage tool and an # https library that is out of date in the base image. @@ -18,53 +18,56 @@ RUN pip install --upgrade pip \ && python --version RUN pip install coverage==5.5 && \ - pip install in_place==0.5.0 && \ - pip install pathos==0.2.7 + pip install in_place==1.0.1 && \ + pip install pathos==0.3.4 # download StringTie software and untar it -RUN STRINGTIE_V='2.1.5' && \ - mkdir /kb/deployment/bin/modules && \ +RUN STRINGTIE_V='2.1.4' && \ + mkdir -p /kb/deployment/bin/modules && \ cd /kb/deployment/bin/modules && \ - mkdir StringTie && cd StringTie && \ - wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-${STRINGTIE_V}.Linux_x86_64.tar.gz &&\ + mkdir -p StringTie && cd StringTie && \ + wget https://ccb.jhu.edu/software/stringtie/dl/stringtie-${STRINGTIE_V}.Linux_x86_64.tar.gz && \ tar xvfz stringtie-${STRINGTIE_V}.Linux_x86_64.tar.gz && \ cd stringtie-${STRINGTIE_V}.Linux_x86_64 && \ - mkdir /kb/deployment/bin/StringTie && \ - cp -R stringtie /kb/deployment/bin/StringTie/stringtie + mkdir -p /kb/deployment/bin/StringTie && \ + cp -R stringtie /kb/deployment/bin/StringTie/stringtie && \ + /kb/deployment/bin/StringTie/stringtie --version # ----------------------------------------- # download prepDE script RUN cd /kb/deployment/bin/modules && \ - mkdir prepDE && cd prepDE && \ - wget http://ccb.jhu.edu/software/stringtie/dl/prepDE.py3 &&\ - mkdir /kb/deployment/bin/prepDE && \ + mkdir -p prepDE && cd prepDE && \ + wget https://raw.githubusercontent.com/gpertea/stringtie/master/prepDE.py3 && \ + mkdir -p /kb/deployment/bin/prepDE && \ cp -R prepDE.py3 /kb/deployment/bin/prepDE/prepDE.py && \ - chmod 777 /kb/deployment/bin/prepDE/prepDE.py + chmod 755 /kb/deployment/bin/prepDE/prepDE.py # ----------------------------------------- # download gffread script -RUN GFFREAD_V='0.12.6' && \ +RUN GFFREAD_V='0.12.7' && \ cd /kb/deployment/bin/modules && \ - mkdir gffread && cd gffread && \ - wget http://ccb.jhu.edu/software/stringtie/dl/gffread-${GFFREAD_V}.Linux_x86_64.tar.gz &&\ + mkdir -p gffread && cd gffread && \ + wget https://ccb.jhu.edu/software/stringtie/dl/gffread-${GFFREAD_V}.Linux_x86_64.tar.gz && \ tar xvfz gffread-${GFFREAD_V}.Linux_x86_64.tar.gz && \ cd gffread-${GFFREAD_V}.Linux_x86_64 && \ - mkdir /kb/deployment/bin/gffread && \ - cp -R gffread /kb/deployment/bin/gffread/gffread + mkdir -p /kb/deployment/bin/gffread && \ + cp -R gffread /kb/deployment/bin/gffread/gffread && \ + chmod 755 /kb/deployment/bin/gffread/gffread # ----------------------------------------- # download gffcompare script -RUN GFFCOMP_V='0.12.2' && \ +RUN GFFCOMP_V='0.12.10' && \ cd /kb/deployment/bin/modules && \ - mkdir gffcompare && cd gffcompare && \ - wget http://ccb.jhu.edu/software/stringtie/dl/gffcompare-${GFFCOMP_V}.Linux_x86_64.tar.gz &&\ - tar xvfz gffcompare-${GFFCOMP_V}.Linux_x86_64.tar.gz && \ - cd gffcompare-${GFFCOMP_V}.Linux_x86_64 && \ - mkdir /kb/deployment/bin/gffcompare && \ - cp -R gffcompare /kb/deployment/bin/gffcompare/gffcompare + mkdir -p gffcompare && cd gffcompare && \ + wget https://ccb.jhu.edu/software/stringtie/dl/gffcompare-${GFFCOMP_V}.Linux_x86_64.tar.gz && \ + tar xvfz gffcompare-${GFFCOMP_V}.Linux_x86_64.tar.gz && \ + cd gffcompare-${GFFCOMP_V}.Linux_x86_64 && \ + mkdir -p /kb/deployment/bin/gffcompare && \ + cp -R gffcompare /kb/deployment/bin/gffcompare/gffcompare && \ + chmod 755 /kb/deployment/bin/gffcompare/gffcompare # -----------------------------------------