Merge branch 'release-5.73-104.0' into faster-lookup

ebi-pf-team · Feb 3, 2025 · 5c5fc2e · 5c5fc2e
2 parents fc7c119 + 39de703
commit 5c5fc2e
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diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 [![Build](https://github.com/ebi-pf-team/interproscan/actions/workflows/build-test.yml/badge.svg)](https://github.com/ebi-pf-team/interproscan/actions/workflows/build-test.yml)
-[![Docker Image Version (tag)](https://img.shields.io/docker/v/interpro/interproscan/5.72-103.0)](https://hub.docker.com/r/interpro/interproscan)
+[![Docker Image Version (tag)](https://img.shields.io/docker/v/interpro/interproscan/5.73-104.0)](https://hub.docker.com/r/interpro/interproscan)
 
 # InterProScan
 

diff --git a/core/business/pom.xml b/core/business/pom.xml
@@ -5,13 +5,13 @@
     <parent>
         <groupId>uk.ac.ebi.interpro.scan</groupId>
         <artifactId>interproscan</artifactId>
-        <version>5.72-103.0</version>
+        <version>5.73-104.0</version>
     </parent>
 
     <modelVersion>4.0.0</modelVersion>
 
     <artifactId>interproscan-business</artifactId>
-    <version>5.72-103.0</version>
+    <version>5.73-104.0</version>
 
     <packaging>jar</packaging>
     <name>InterProScan Business Logic</name>
@@ -35,14 +35,14 @@
         <dependency>
             <groupId>uk.ac.ebi.interpro.scan</groupId>
             <artifactId>interproscan-persistence</artifactId>
-            <version>5.72-103.0</version>
+            <version>5.73-104.0</version>
         </dependency>
 
 
         <dependency>
             <groupId>uk.ac.ebi.interpro.scan</groupId>
             <artifactId>precalc-match-client</artifactId>
-            <version>5.72-103.0</version>
+            <version>5.73-104.0</version>
         </dependency>
 
         <dependency>

diff --git a/core/generic-jpa-dao/pom.xml b/core/generic-jpa-dao/pom.xml
@@ -5,13 +5,13 @@
     <parent>
         <groupId>uk.ac.ebi.interpro.scan</groupId>
         <artifactId>interproscan</artifactId>
-        <version>5.72-103.0</version>
+        <version>5.73-104.0</version>
     </parent>
 
     <modelVersion>4.0.0</modelVersion>
 
     <artifactId>generic-jpa-dao</artifactId>
-    <version>5.72-103.0</version>
+    <version>5.73-104.0</version>
 
     <packaging>jar</packaging>
 
@@ -37,7 +37,7 @@
         <dependency>
             <groupId>uk.ac.ebi.interpro.scan</groupId>
             <artifactId>interproscan-util</artifactId>
-            <version>5.72-103.0</version>
+            <version>5.73-104.0</version>
         </dependency>
 
         <!-- Hibernate -->

diff --git a/core/io/pom.xml b/core/io/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>interproscan</artifactId>
         <groupId>uk.ac.ebi.interpro.scan</groupId>
-        <version>5.72-103.0</version>
+        <version>5.73-104.0</version>
     </parent>
 
     <modelVersion>4.0.0</modelVersion>
@@ -14,21 +14,21 @@
     <packaging>jar</packaging>
 
     <name>InterProScan IO</name>
-    <version>5.72-103.0</version>
+    <version>5.73-104.0</version>
     <description>InterProScan IO</description>
     <url>http://www.ebi.ac.uk/interpro/</url>
 
     <dependencies>
         <dependency>
             <groupId>uk.ac.ebi.interpro.scan</groupId>
             <artifactId>interproscan-util</artifactId>
-            <version>5.72-103.0</version>
+            <version>5.73-104.0</version>
         </dependency>
 
         <dependency>
             <groupId>uk.ac.ebi.interpro.scan</groupId>
             <artifactId>interproscan-model</artifactId>
-            <version>5.72-103.0</version>
+            <version>5.73-104.0</version>
         </dependency>
 
         <dependency>

diff --git a/core/jms-implementation/pom.xml b/core/jms-implementation/pom.xml
@@ -5,12 +5,12 @@
     <parent>
         <groupId>uk.ac.ebi.interpro.scan</groupId>
         <artifactId>interproscan</artifactId>
-        <version>5.72-103.0</version>
+        <version>5.73-104.0</version>
     </parent>
 
     <modelVersion>4.0.0</modelVersion>
     <artifactId>jms-implementation</artifactId>
-    <version>5.72-103.0</version>
+    <version>5.73-104.0</version>
 
     <packaging>jar</packaging>
 
@@ -53,7 +53,7 @@
         <dependency>
             <groupId>uk.ac.ebi.interpro.scan</groupId>
             <artifactId>interproscan-management</artifactId>
-            <version>5.72-103.0</version>
+            <version>5.73-104.0</version>
         </dependency>
 
         <dependency>

diff --git a/core/jms-implementation/src/main/java/uk/ac/ebi/interpro/scan/jms/main/Run.java b/core/jms-implementation/src/main/java/uk/ac/ebi/interpro/scan/jms/main/Run.java
@@ -141,7 +141,7 @@ public static void main(String[] args) {
 
             ArrayList<String> analysesHelpInformation = new ArrayList<>();
 
-            String i5Version = "5.72-103.0";
+            String i5Version = "5.73-104.0";
             String i5BuildType = "64-Bit";
 
             if (parsedCommandLine.hasOption(I5Option.VERSION.getLongOpt())) {

diff --git a/core/jms-implementation/src/main/resources/application-default.properties b/core/jms-implementation/src/main/resources/application-default.properties
@@ -87,16 +87,16 @@ binary.getorf.path=${bin.directory}/nucleotide/getorf
 binary.esltranslate.path=${bin.directory}/nucleotide/esl-translate
 
 # AntiFam
-antifam.signature.library.release=7.0
-antifam.hmm.path=${data.directory}/antifam/7.0/AntiFam.hmm
+antifam.signature.library.release=8.0
+antifam.hmm.path=${data.directory}/antifam/8.0/AntiFam.hmm
 hmmer3.hmmsearch.cpu.switch.antifam=--cpu 1
 hmmer3.hmmsearch.switches.antifam=--cut_ga
 
 #CDD
-cdd.signature.library.release=3.20
-cdd.signature.list.path=${data.directory}/cdd/3.20/data/cddid.tbl
-cdd.library.path=${data.directory}/cdd/3.20/db/Cdd_NCBI
-cdd.data.path=${data.directory}/cdd/3.20/data
+cdd.signature.library.release=3.21
+cdd.signature.list.path=${data.directory}/cdd/3.21/data/cddid.tbl
+cdd.library.path=${data.directory}/cdd/3.21/db/Cdd_NCBI
+cdd.data.path=${data.directory}/cdd/3.21/data
 binary.rpsblast.path=${bin.directory}/cdd/rpsblast
 rpsblast.switches.cdd=-evalue 0.01 -seg no -outfmt 11
 binary.rpsbproc.path=${bin.directory}/cdd/rpsbproc
@@ -145,8 +145,8 @@ binary.mobidb.path=${bin.directory}/mobidb/idrpred-cli.py
 mobidb.binary.cpu.switches=--threads 1
 
 # NCBIfam
-ncbifam.signature.library.release=15.0
-ncbifam.hmm.path=${data.directory}/ncbifam/15.0/ncbifam.hmm
+ncbifam.signature.library.release=17.0
+ncbifam.hmm.path=${data.directory}/ncbifam/17.0/ncbifam.hmm
 hmmer3.hmmsearch.switches.ncbifam=-Z 61295632 --cut_tc
 hmmer3.hmmsearch.cpu.switch.ncbifam=--cpu 1
 
@@ -163,11 +163,11 @@ hmmer3.hmmsearch.switches.panther=-Z 65000000 -E 0.001 --domE 0.00000001 --incdo
 panther.binary.switches=-e 0.00000001 --keep
 
 # PFam
-pfam-a.signature.library.release=37.1
-pfam-a.hmm.path=${data.directory}/pfam/37.1/pfam_a.hmm
-pfam-a.seed.path=${data.directory}/pfam/37.1/pfam_a.seed
-pfam-clans.path=${data.directory}/pfam/37.1/pfam_clans
-pfam-a.dat.path=${data.directory}/pfam/37.1/pfam_a.dat
+pfam-a.signature.library.release=37.2
+pfam-a.hmm.path=${data.directory}/pfam/37.2/pfam_a.hmm
+pfam-a.seed.path=${data.directory}/pfam/37.2/pfam_a.seed
+pfam-clans.path=${data.directory}/pfam/37.2/pfam_clans
+pfam-a.dat.path=${data.directory}/pfam/37.2/pfam_a.dat
 hmmer3.hmmsearch.cpu.switch.pfama=--cpu 1
 hmmer3.hmmsearch.switches.pfama=-Z 61295632 --cut_ga
 pfam.min.length=8

diff --git a/core/jms-implementation/support-mini-x86-32/bin/cdd/rpsblast b/core/jms-implementation/support-mini-x86-32/bin/cdd/rpsblast
diff --git a/core/jms-implementation/support-mini-x86-32/bin/pirsf/3.10/pirsf.pl b/core/jms-implementation/support-mini-x86-32/bin/pirsf/3.10/pirsf.pl
@@ -64,7 +64,7 @@
 # Main body
 
 # Check that the hmm files have been properly pressed
-PIRSF::checkHmmFiles($sf_hmm, $hmmer_path);
+# PIRSF::checkHmmFiles($sf_hmm, $hmmer_path);
 
 # Read the PIRSF data file.
 my ($pirsf_data, $children) = PIRSF::read_pirsf_dat($pirsf_dat);