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abims
e-infra
gga_load_data
Commits
dce8482b
Commit
dce8482b
authored
3 years ago
by
Arthur Le Bars
Committed by
Loraine Gueguen
2 years ago
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typo fix: debug logging to display analysis IDs used by galaxy tools (blast interpro workflow)
parent
b4965f39
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2 merge requests
!47
v2.5.0
,
!34
WIP: blast and interpro workflow
Changes
1
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gga_run_workflow_phaeo_blast_interpro.py
+4
-4
4 additions, 4 deletions
gga_run_workflow_phaeo_blast_interpro.py
with
4 additions
and
4 deletions
gga_run_workflow_phaeo_blast_interpro.py
+
4
−
4
View file @
dce8482b
...
...
@@ -509,7 +509,7 @@ if __name__ == "__main__":
# It affects the first analysis found (genome analysis) instead of the provided ones below
# Use --verbose argument to get debug logging to display the analysis IDs
logging
.
debug
(
"
Blastp analysis id for organism 1 ({0}): {1}
"
.
format
(
genus_species
,
org_wf_param
.
blastp_analysis_id
))
logging
.
debug
(
"
Blastx analysis id for organism 1 ({0}): {1}
"
.
format
(
genus_species
,
org_wf_param
.
blast
p
_analysis_id
))
logging
.
debug
(
"
Blastx analysis id for organism 1 ({0}): {1}
"
.
format
(
genus_species
,
org_wf_param
.
blast
x
_analysis_id
))
logging
.
debug
(
"
InterProScan analysis id for organism 1 ({0}): {1}
"
.
format
(
genus_species
,
org_wf_param
.
interpro_analysis_id
))
# Input files have no parameters (they are set via assigning the hda IDs in the datamap parameter of the bioblend method)
...
...
@@ -599,12 +599,12 @@ if __name__ == "__main__":
# It affects the first analysis found (genome analysis) instead of the provided ones below
# Use --verbose argument to get debug logging to display the analysis IDs
logging
.
debug
(
"
Blastp analysis id for organism 1 ({0}, {1}): {2}
"
.
format
(
genus_species
,
strain_sex_org1
,
sp_wf_param_org1
.
blastp_analysis_id
))
logging
.
debug
(
"
Blastx analysis id for organism 1 ({0}, {1}): {2}
"
.
format
(
genus_species
,
strain_sex_org1
,
sp_wf_param_org1
.
blast
p
_analysis_id
))
logging
.
debug
(
"
Blastx analysis id for organism 1 ({0}, {1}): {2}
"
.
format
(
genus_species
,
strain_sex_org1
,
sp_wf_param_org1
.
blast
x
_analysis_id
))
logging
.
debug
(
"
InterProScan analysis id for organism 1 ({0}, {1}): {2}
"
.
format
(
genus_species
,
strain_sex_org1
,
sp_wf_param_org1
.
interpro_analysis_id
))
logging
.
debug
(
"
Blastp analysis id for organism 2 ({0}, {1}): {2}
"
.
format
(
genus_species
,
strain_sex_org2
,
sp_wf_param_org2
.
blastp_analysis_id
))
logging
.
debug
(
"
Blastx analysis id for organism 2 ({0}, {1}): {2}
"
.
format
(
genus_species
,
strain_sex_org2
,
sp_wf_param_org2
.
blast
p
_analysis_id
))
logging
.
debug
(
"
Blastx analysis id for organism 2 ({0}, {1}): {2}
"
.
format
(
genus_species
,
strain_sex_org2
,
sp_wf_param_org2
.
blast
x
_analysis_id
))
logging
.
debug
(
"
InterProScan analysis id for organism 2 ({0}, {1}): {2}
"
.
format
(
genus_species
,
strain_sex_org2
,
sp_wf_param_org2
.
interpro_analysis_id
))
# Input files have no parameters (they are set via assigning the hda IDs in the datamap parameter of the bioblend method)
workflow_parameters
[
constants_phaeo
.
WF_BLAST_INTERPRO_2_ORG_INPUT_BLASTP_ORG1
]
=
{}
workflow_parameters
[
constants_phaeo
.
WF_BLAST_INTERPRO_2_ORG_INPUT_BLASTP_ORG2
]
=
{}
...
...
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