DoBlastzChainNet.pl: Difference between revisions
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==Install scripts and kent command line utilities== | ==Install scripts and kent command line utilities== | ||
<pre> | |||
<nowiki> | |||
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' | |||
</nowiki> | |||
</pre> | |||
Revision as of 00:03, 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
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'
