From 915a66b90989921fa798e79f5e3cecaf4578e01c Mon Sep 17 00:00:00 2001 From: Tiago Grego Date: Wed, 6 Dec 2023 13:24:15 +0000 Subject: [PATCH] update hamap and prosite properties to 2023_05 --- .../resources/application-default.properties | 22 +++++++++---------- .../support-mini-x86-32/installer.properties | 12 +++++----- .../interproscan.properties | 2 +- 3 files changed, 18 insertions(+), 18 deletions(-) diff --git a/core/jms-implementation/src/main/resources/application-default.properties b/core/jms-implementation/src/main/resources/application-default.properties index 99f517de1..99b089ba2 100644 --- a/core/jms-implementation/src/main/resources/application-default.properties +++ b/core/jms-implementation/src/main/resources/application-default.properties @@ -134,10 +134,10 @@ hmmer3.hmmsearch.switches.funfam=-Z 65245 --cut_tc # HAMAP binary.hamap.pfsearch.wrapperpath=${bin.directory}/prosite/pfsearch_wrapper.py -hamap.signature.library.release=2023_01 -hamap.profile.models.path=${data.directory}/hamap/2023_01/hamap.prf -hamap.profile.models.dir=${data.directory}/hamap/2023_01/profiles -hamap.hmm.path=${data.directory}/hamap/2023_01/hamap.hmm.lib +hamap.signature.library.release=2023_05 +hamap.profile.models.path=${data.directory}/hamap/2023_05/hamap.prf +hamap.profile.models.dir=${data.directory}/hamap/2023_05/profiles +hamap.hmm.path=${data.directory}/hamap/2023_05/hamap.hmm.lib hmmer3.hmmsearch.cpu.switch.hmmfilter=--cpu 1 hmmer3.hmmsearch.switches.hmmfilter=-E 100 --domE 100 --incE 100 --incdomE 100 pfsearchv3.hamap.binary.switches=-f -o 7 @@ -213,17 +213,17 @@ fingerprintscan.binary.switches=-e 0.0001 -d 10 -E 257043 84355444 -fj -o 15 # PROSITE # Note: Correct PROSITE binary distribution for your platform can be downloaded: ftp://ftp.expasy.org/databases/prosite/ps_scan/ -prosite.patterns.signature.library.release=2022_05 -prosite.profiles.signature.library.release=2022_05 +prosite.patterns.signature.library.release=2023_05 +prosite.profiles.signature.library.release=2023_05 binary.prosite.psscan.pl.path=${bin.directory}/prosite/ps_scan.pl binary.prosite.pfscanv3.path=${bin.directory}/prosite/pfscanV3 binary.prosite.pfsearchv3.path=${bin.directory}/prosite/pfsearchV3 binary.prosite.runprosite.path=${bin.directory}/prosite/runprosite.py -prosite.patterns.models.path=${data.directory}/prosite/2022_05/prosite_patterns.dat -prosite.profiles.models.path=${data.directory}/prosite/2022_05/prosite_profiles.dat -prosite.profiles.models.dir=${data.directory}/prosite/2022_05/prosite_profiles -prosite.evaluator.models.path=${data.directory}/prosite/2022_05/evaluator.dat -prosite.profiles.skip.flagged.profiles=${data.directory}/prosite/2022_05/skip_flagged_profiles.txt +prosite.patterns.models.path=${data.directory}/prosite/2023_05/prosite_patterns.dat +prosite.profiles.models.path=${data.directory}/prosite/2023_05/prosite_profiles.dat +prosite.profiles.models.dir=${data.directory}/prosite/2023_05/prosite_profiles +prosite.evaluator.models.path=${data.directory}/prosite/2023_05/evaluator.dat +prosite.profiles.skip.flagged.profiles=${data.directory}/prosite/2023_05/skip_flagged_profiles.txt psscan.prosite.profiles.usepfsearch=true pfsearchv3.binary.switches.prosite.profiles=-f -o 7 pfsearchv3.cpu.switch.prosite.profiles=-t 4 diff --git a/core/jms-implementation/support-mini-x86-32/installer.properties b/core/jms-implementation/support-mini-x86-32/installer.properties index 4ea49cab1..a56d58a9a 100644 --- a/core/jms-implementation/support-mini-x86-32/installer.properties +++ b/core/jms-implementation/support-mini-x86-32/installer.properties @@ -32,8 +32,8 @@ gene3d.cath.family.names=data/gene3d/4.3.0/cath-family-names.txt gene3d.model2sf_map.path=data/gene3d/4.3.0/model_to_family_map.tsv # HAMAP -hamap.signature.library.release=2023_01 -hamap.profile.models.path=data/hamap/2023_01/hamap.prf +hamap.signature.library.release=2023_05 +hamap.profile.models.path=data/hamap/2023_05/hamap.prf # MobiDB mobidb.signature.library.release=2.0 @@ -63,10 +63,10 @@ prints.kdat.path=data/prints/42.0/prints.kdat prints.pval.path=data/prints/42.0/prints.pval # Prosite -prosite.patterns.signature.library.release=2022_05 -prosite.patterns.models.path=data/prosite/2022_05/prosite_patterns.dat -prosite.profiles.signature.library.release=2022_05 -prosite.profiles.models.path=data/prosite/2022_05/prosite_profiles.dat +prosite.patterns.signature.library.release=2023_05 +prosite.patterns.models.path=data/prosite/2023_05/prosite_patterns.dat +prosite.profiles.signature.library.release=2023_05 +prosite.profiles.models.path=data/prosite/2023_05/prosite_profiles.dat # SFLD sfld.signature.library.release=4 diff --git a/core/jms-implementation/support-mini-x86-32/interproscan.properties b/core/jms-implementation/support-mini-x86-32/interproscan.properties index 1f24bf4a4..e359f7613 100644 --- a/core/jms-implementation/support-mini-x86-32/interproscan.properties +++ b/core/jms-implementation/support-mini-x86-32/interproscan.properties @@ -22,7 +22,7 @@ binary.hmmer33.path=${bin.directory}/hmmer/hmmer3/3.3 #################################### antifam.hmm.path=${data.directory}/antifam/7.0/AntiFam.hmm gene3d.hmm.path=${data.directory}/gene3d/4.3.0/gene3d_main.hmm -hamap.hmm.path=${data.directory}/hamap/2023_01/hamap.hmm.lib +hamap.hmm.path=${data.directory}/hamap/2023_05/hamap.hmm.lib ncbifam.hmm.path=${data.directory}/ncbifam/13.0/ncbifam.hmm panther.hmm.path=${data.directory}/panther/18.0/famhmm/binHmm pfam-a.hmm.path=${data.directory}/pfam/36.0/pfam_a.hmm