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Commit 2717c181 authored by Susheel Busi's avatar Susheel Busi
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cleaned up path exporting for rule/ANALYSIS_RULES and added to the config/CONFIG.yaml file

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2019_GDB/config/CONFIG.yaml
+ 11
− 2
View file @ 2717c181
# steps: "assembly_annotation mapping metaT mmseq binning taxonomy analysis"
steps: "binning taxonomy"
steps: "binning taxonomy analysis"
data_dir: "data"
results_dir: "results"
db_dir: "dbs"
......@@ -91,7 +91,8 @@ rebaler:
threads: 28
diamond:
threads: 28
db: "/mnt/isilon/projects/ecosystem_biology/NOMIS/DIAMOND/new_nr.dmnd"
#db: "/mnt/isilon/projects/ecosystem_biology/NOMIS/DIAMOND/new_nr.dmnd"
db: "/work/projects/ecosystem_biology/local_tools/databases/nr_uniprot_trembl.dmnd"
metaspades:
threads: 28
mmseq2:
......@@ -151,3 +152,11 @@ mmseqs:
createdb: "/home/users/sbusi/apps/mmseqs/bin/mmseqs createdb"
rbh: "/home/users/sbusi/apps/mmseqs/bin/mmseqs rbh"
convertalis: "/home/users/sbusi/apps/mmseqs/bin/mmseqs convertalis"
# Paths to CASC and minced for CRISPR
CASC:
PATH: "$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/bin"
PERL5LIB: "/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/lib/site_perl"
minced:
PATH: "$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/minced/"
2019_GDB/rules/ANALYSIS_RULES
+ 5
− 4
View file @ 2717c181
......@@ -165,11 +165,12 @@ rule casc:
shell:
"""
(date &&\
export PATH=$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/bin &&\
export PERL5LIB=/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/lib/site_perl
export PATH={config[CASC][PATH]} &&\
export PERL5LIB={config[CASC][PERL5LIB]} &&\
casc -i {input} -o $(dirname {output.cas1}) -n 12 --conservative &&\
echo $(basename -s ".results.txt" {output.cas1}) >> {output.cas2} &&\
awk '$8 == "true" {{sum += $2}} END {{print sum}}' {output.cas1} >> {output.cas2} &&\
# awk '$8 == "true" {{sum += $2}} END {{print sum}}' {output.cas1} >> {output.cas2} &&\
cat {output.cas1}) | awk '$8 == "true" {{sum += $2}} END {{print sum}}' >> {output.cas2} &&\
date) &> >(tee {log})
"""
......@@ -184,7 +185,7 @@ rule minced:
shell:
"""
(date &&\
export PATH=$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/minced/ &&\
export PATH={config[minced][PATH]} &&\
minced {input} {output.mn1} {output.mn2} &&\
echo $(basename -s ".txt" {output.mn1}) >> minced_CRISPR_output.txt &&\
grep -c 'CRISPR' {output.mn1} >> minced_CRISPR_output.txt &&\
......
config/CONFIG.yaml
+ 11
− 2
View file @ 2717c181
# steps: "assembly_annotation mapping metaT mmseq binning taxonomy analysis"
steps: "binning taxonomy"
steps: "binning taxonomy analysis"
data_dir: "data"
results_dir: "results"
db_dir: "dbs"
......@@ -91,7 +91,8 @@ rebaler:
threads: 28
diamond:
threads: 28
db: "/mnt/isilon/projects/ecosystem_biology/NOMIS/DIAMOND/new_nr.dmnd"
#db: "/mnt/isilon/projects/ecosystem_biology/NOMIS/DIAMOND/new_nr.dmnd"
db: "/work/projects/ecosystem_biology/local_tools/databases/nr_uniprot_trembl.dmnd"
metaspades:
threads: 28
mmseq2:
......@@ -151,3 +152,11 @@ mmseqs:
createdb: "/home/users/sbusi/apps/mmseqs/bin/mmseqs createdb"
rbh: "/home/users/sbusi/apps/mmseqs/bin/mmseqs rbh"
convertalis: "/home/users/sbusi/apps/mmseqs/bin/mmseqs convertalis"
# Paths to CASC and minced for CRISPR
CASC:
PATH: "$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/bin"
PERL5LIB: "/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/lib/site_perl"
minced:
PATH: "$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/minced/"
rules/ANALYSIS_RULES
+ 5
− 4
View file @ 2717c181
......@@ -165,11 +165,12 @@ rule casc:
shell:
"""
(date &&\
export PATH=$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/bin &&\
export PERL5LIB=/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/lib/site_perl
export PATH={config[CASC][PATH]} &&\
export PERL5LIB={config[CASC][PERL5LIB]} &&\
casc -i {input} -o $(dirname {output.cas1}) -n 12 --conservative &&\
echo $(basename -s ".results.txt" {output.cas1}) >> {output.cas2} &&\
awk '$8 == "true" {{sum += $2}} END {{print sum}}' {output.cas1} >> {output.cas2} &&\
# awk '$8 == "true" {{sum += $2}} END {{print sum}}' {output.cas1} >> {output.cas2} &&\
cat {output.cas1}) | awk '$8 == "true" {{sum += $2}} END {{print sum}}' >> {output.cas2} &&\
date) &> >(tee {log})
"""
......@@ -184,7 +185,7 @@ rule minced:
shell:
"""
(date &&\
export PATH=$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/minced/ &&\
export PATH={config[minced][PATH]} &&\
minced {input} {output.mn1} {output.mn2} &&\
echo $(basename -s ".txt" {output.mn1}) >> minced_CRISPR_output.txt &&\
grep -c 'CRISPR' {output.mn1} >> minced_CRISPR_output.txt &&\
......
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