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Content onboarding scripts #26

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merged 6 commits into from
Oct 22, 2019
Merged

Content onboarding scripts #26

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fc8b836
Add content_onboarding_scripts
mpoelchau Sep 25, 2019
9f75e6e
Make additional scripts executable
mpoelchau Sep 25, 2019
f550f93
Add additional scripts to PATH
mpoelchau Sep 25, 2019
0770b97
fixed rubocop validation issues
childers Oct 17, 2019
3959e00
fixing the new export command.
childers Oct 17, 2019
1f9fb4d
Merge branch 'kenttools' into content_onboarding_scripts
childers Oct 22, 2019
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15 changes: 13 additions & 2 deletions Vagrantfile
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Original file line number Diff line number Diff line change
Expand Up @@ -207,8 +207,16 @@ Vagrant.configure('2') do |config|
cd /home/vagrant
git clone https://github.com/NAL-i5K/wiggle-tools
git clone https://github.com/NAL-i5K/bam_to_bigwig
git clone https://gitlab.com/i5k_Workspace/apollo2_data_build_scripts.git
git clone https://github.com/GMOD/jbrowse
git clone https://github.com/NAL-i5K/content_onboarding_scripts
git clone https://github.com/GMOD/jbrowse

#Make other tools executable
sudo chmod +x /home/vagrant/wiggle-tools/GCcontent2bigwig.py
sudo chmod +x /home/vagrant/wiggle-tools/gap2bigwig.py
sudo chmod +x /home/vagrant/bam_to_bigwig/bam_to_bigwig.py
sudo chmod +x /home/vagrant/content_onboarding_scripts/bin/add_metadata_to_GC_gap_bigwig_tracks.pl
sudo chmod +x /home/vagrant/content_onboarding_scripts/bin/createOrganism.py
sudo chmod -R +x /home/vagrant/jbrowse/bin

# Create directories used
mkdir -p /app/data/blat
Expand All @@ -217,6 +225,9 @@ Vagrant.configure('2') do |config|
mkdir -p /app/data/working-files
mkdir -p /app/data/tools

#Add tools to PATH
export PATH=$PATH:/home/vagrant/wiggle-tools:/home/vagrant/bam_to_bigwig:/home/vagrant/content_onboarding_scripts/bin:/home/vagrant/jbrowse/bin

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This only sets $PATH for the active session. Once we reset the session, this $PATH is lost.


# install the Kent tools for data processing

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