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Add SRA toolkit #48

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Add SRA toolkit #48

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10 changes: 10 additions & 0 deletions Dockerfile
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Expand Up @@ -163,6 +163,16 @@ RUN export DEBIAN_FRONTEND=noninteractive && \
rm -r hisat2-$HISAT_VERSION/example && \
echo "PATH=\$PATH:~/hisat2-$HISAT_VERSION" >> ~/.bash_profile && \

echo "Installing sra-toolkit..." && \
SRA_TOOLKIT_VERSION=2.8.0 && \
SRA_TOOLKIT_SHA1SUM=fcfcacde92e0d4633ea9ba23fec5945f31a32c39 && \
wget -q ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/$SRA_TOOLKIT_VERSION/sratoolkit.$SRA_TOOLKIT_VERSION-ubuntu64.tar.gz -O sra_toolkit.tar.gz && \
echo "$SRA_TOOLKIT_SHA1SUM *sra_toolkit.tar.gz" | sha1sum -c - && \
mkdir sra_toolkit-$SRA_TOOLKIT_VERSION && \
tar -xf sra_toolkit.tar.gz --directory sra_toolkit-$SRA_TOOLKIT_VERSION --strip-components=1 && \
rm sra_toolkit.tar.gz && \
echo "PATH=\$PATH:~/sra_toolkit-$SRA_TOOLKIT_VERSION/bin" >> ~/.bash_profile && \

echo "Installing R packages..." && \
sudo Rscript --slave --no-save --no-restore-history -e " \
package_list = c( \
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