Ncbi-fcs: Difference between revisions
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
* | * GXDB_LOC - database directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
* unset PYTHONHOME | * unset PYTHONHOME after loading the ncbi-fcs module | ||
* request at least 512 GiB memory to hold the database and accessory files. | |||
* copy the full "gxdb" database to the slurm $TMPDIR | |||
* set $GXDB_LOC environmental variable to point to $TMPDIR | |||
cp -r "$GXDB_LOC/gxdb" $TMPDIR/gxdb | |||
export GXDB_LOC=$TMPDIR | |||
Latest revision as of 19:25, 28 February 2025
Description
Foreign Contamination Screening caller scripts and documentation.
Environment Modules
Run module spider ncbi-fcs to find out what environment modules are available for this application.
System Variables
- HPC_NCBI-FCS_DIR - installation directory
- HPC_NCBI-FCS_BIN - executable directory
- GXDB_LOC - database directory
Additional Information
- unset PYTHONHOME after loading the ncbi-fcs module
- request at least 512 GiB memory to hold the database and accessory files.
- copy the full "gxdb" database to the slurm $TMPDIR
- set $GXDB_LOC environmental variable to point to $TMPDIR
cp -r "$GXDB_LOC/gxdb" $TMPDIR/gxdb export GXDB_LOC=$TMPDIR