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Fix for edirect tools #3

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Fix for edirect tools #3

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f5b0bda
Add anaconda bin directory at the end of PATH to use non-anaconda perl
boratyng Dec 28, 2018
aee2308
Updated plink2 version
boratyng Dec 28, 2018
68ea635
Uncomented testing edirect
boratyng Dec 28, 2018
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8 changes: 4 additions & 4 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,7 @@ RUN wget -q https://repo.anaconda.com/archive/Anaconda2-5.3.1-Linux-x86_64.sh &&
rm ./Anaconda2-5.3.1-Linux-x86_64.sh && \
echo -e "export PATH=\$PATH:/opt/anaconda2/bin\nexport JAVA_HOME=/opt/anaconda2" > /etc/profile.d/anaconda2.sh && \
chmod 755 /etc/profile.d/anaconda2.sh
ENV PATH="/opt/anaconda2/bin:${PATH}"
ENV PATH="${PATH}:/opt/anaconda2/bin"

###############
# GATK, BWA, minimap2, bowtie2, HMMER, DESeq2
Expand Down Expand Up @@ -184,9 +184,9 @@ ENV PATH="/opt/START-2.6.0a/bin:${PATH}"

###############
# plink-ng
RUN wget -q http://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_20181028.zip && \
unzip -qq plink2_linux_x86_64_20181028.zip && \
rm plink2_linux_x86_64_20181028.zip && \
RUN wget -q http://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_20181227.zip && \
unzip -qq plink2_linux_x86_64_20181227.zip && \
rm plink2_linux_x86_64_20181227.zip && \
mv ./plink2 /usr/bin

###############
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4 changes: 2 additions & 2 deletions Makefile
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Expand Up @@ -25,8 +25,8 @@ check:
time docker exec `docker ps -lq` /bin/bash -c "printenv BLASTDB"
time docker exec `docker ps -lq` blastn -version
time docker exec `docker ps -lq` magicblast -version
#time docker exec `docker ps -lq` installconfirm
#time docker exec `docker ps -lq` efetch -db nucleotide -id u00001 -format fasta
time docker exec `docker ps -lq` installconfirm
time docker exec `docker ps -lq` efetch -db nucleotide -id u00001 -format fasta
#time docker exec `docker ps -lq` get_species_taxids.sh -n squirrel
#time docker exec `docker ps -lq` update_blastdb.pl --source gcp --showall
#time docker exec `docker ps -lq` update_blastdb.pl --source gcp taxdb
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