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Merged
Cyrus-Shahnam merged 1 commit into from
Sep 2, 2025
Merged

updated to currect public tool 2.1.4 #85

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55 changes: 29 additions & 26 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -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
Expand All @@ -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# https library that is out of date in the base image.
Expand All @@ -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

# -----------------------------------------

Expand Down