DoBlastzChainNet.pl: Difference between revisions
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setup, the kent command line binaries and these scripts are going to reside in '''/data/bin/''' | setup, the kent command line binaries and these scripts are going to reside in '''/data/bin/''' | ||
and '''/data/scripts/'''. This is merely a style custom to keep scripts separate | and '''/data/scripts/'''. This is merely a style custom to keep scripts separate | ||
from binaries, this is not strictly necessary. | from binaries, this is not strictly necessary to keep them separate. | ||
<pre> | <pre> | ||
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</nowiki> | </nowiki> | ||
</pre> | </pre> | ||
==PATH setup== | |||
[[Category:Cluster FAQ]] | [[Category:Cluster FAQ]] | ||
[[Category:Technical FAQ]] | [[Category:Technical FAQ]] | ||
Revision as of 02:36, 6 April 2018
Prerequisites
This discussion assumes you are familiar with Unix shell command line programming and scripting. You will be encountering and interacting with csh/tcsh, bash, perl, and python scripting languages. You will need at least one computer with several CPU cores, preferably a multiple compute cluster system or equivalent in a cloud computing environment.
Parasol Job Control System
The scripts and programs used here expect to find the Parasol_job_control_system in place and operational.
Install scripts and kent command line utilities
This is a bit of a kludge at this time (April 2018), we are working on a cleaner distribution of these scripts. As was mentioned in the Parasol_job_control_system setup, the kent command line binaries and these scripts are going to reside in /data/bin/ and /data/scripts/. This is merely a style custom to keep scripts separate from binaries, this is not strictly necessary to keep them separate.
mkdir -p /data/scripts /data/bin
chmod 755 /data/scripts /data/bin
rsync -a rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ /data/bin/
git archive --remote=git://genome-source.soe.ucsc.edu/kent.git \
--prefix=kent/ HEAD src/hg/utils/automation \
| tar vxf - -C /data/scripts --strip-components=5 \
--exclude='kent/src/hg/utils/automation/incidentDb' \
--exclude='kent/src/hg/utils/automation/configFiles' \
--exclude='kent/src/hg/utils/automation/ensGene' \
--exclude='kent/src/hg/utils/automation/genbank' \
--exclude='kent/src/hg/utils/automation/lastz_D' \
--exclude='kent/src/hg/utils/automation/openStack'
