project_microtrawler/paths at main · baymlab/project_microtrawler · GitHub

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#!/bin/bash

K12GBK="/n/data1/hms/dbmi/baym/arya/ref/Ecoli/K12/GCF_000005845.2_ASM584v2_genomic.gbff.gz"
KlebGBK="/n/data1/hms/dbmi/baym/arya/ref/Kleb/ASM1630v1/GCF_000016305.1_ASM1630v1_genomic.gbff.gz"
FaeciumGBK="/n/data1/hms/dbmi/baym/arya/ref/EntFaecium/ASM973400v2/GCF_009734005.1_ASM973400v2_genomic.gbff.gz"
FaecalisGBK="/n/data1/hms/dbmi/baym/arya/ref/EntFaecalis/ASM2161010v1/GCF_021610105.1_ASM2161010v1_genomic.gbff.gz"
ActBaumanniiGBK="/n/data1/hms/dbmi/baym/arya/ref/ActBaumannii/ASM863263v1/GCF_008632635.1_ASM863263v1_genomic.gbff.gz"
StaphGBK="/n/data1/hms/dbmi/baym/arya/ref/StaphAureus/ASM360985v1/GCF_003609855.1_ASM360985v1_genomic.gbff.gz"
PseudAerugGBK="/n/data1/hms/dbmi/baym/arya/ref/PseudAerug/NCTC10332/GCF_001457615.1_NCTC10332_genomic.gbff.gz"
SalmGBK="/n/data1/hms/dbmi/baym/arya/ref/Salmonella/ASM694v2/GCF_000006945.2_ASM694v2_genomic.gbff.gz"

tooldir="/n/data1/hms/dbmi/baym/arya/tools"

firefox="./hi"
projectdir="/n/data1/hms/dbmi/baym/arya/projects/MicroTrawler"
scriptdir="$projectdir/helper_scripts"

jobdir="/n/data1/hms/dbmi/baym/arya/job_templates"
jobt_0="$jobdir/microt_0.jobtemp"
jobt_1="$jobdir/microt_1.jobtemp"
jobt_1a="$jobdir/microt_1a.jobtemp"
jobt_2="$jobdir/microt_2.jobtemp"
jobt_4="$jobdir/microt_4.jobtemp"