Upgrade to newer version

Dockerfile

@@ -1,14 +1,13 @@
 FROM biocorecrg/debian-perlbrew-pyenv3-java:buster AS builder
 
-ARG IPSCAN_VERSION=5.65-97.0
+ARG IPSCAN_VERSION=5.72-103.0
 
 # Install InterPro
+RUN cd /usr/local; curl --retry 3 --fail --silent --show-error --location --remote-name https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${IPSCAN_VERSION}/alt/interproscan-core-${IPSCAN_VERSION}.tar.gz && \
+  curl --retry 3 --fail --silent --show-error --location --remote-name https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${IPSCAN_VERSION}/alt/interproscan-core-${IPSCAN_VERSION}.tar.gz.md5 && \
+  md5sum -c interproscan-core-${IPSCAN_VERSION}.tar.gz.md5
 
-RUN cd /usr/local; curl --retry 3 --fail --silent --show-error --location --remote-name https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${IPSCAN_VERSION}/interproscan-${IPSCAN_VERSION}-64-bit.tar.gz && \
-	curl --retry 3 --fail --silent --show-error --location --remote-name https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${IPSCAN_VERSION}/interproscan-${IPSCAN_VERSION}-64-bit.tar.gz.md5 && \
-	md5sum -c interproscan-${IPSCAN_VERSION}-64-bit.tar.gz.md5
-
-RUN cd /usr/local; tar zxf interproscan-${IPSCAN_VERSION}-64-bit.tar.gz --exclude "interproscan-${IPSCAN_VERSION}/data" && rm interproscan-${IPSCAN_VERSION}-64-bit.tar.gz interproscan-${IPSCAN_VERSION}-64-bit.tar.gz.md5
+RUN cd /usr/local; tar zxf interproscan-core-${IPSCAN_VERSION}.tar.gz --exclude "interproscan-${IPSCAN_VERSION}/data" && rm interproscan-core-${IPSCAN_VERSION}.tar.gz interproscan-core-${IPSCAN_VERSION}.tar.gz.md5
 
 # Replace interproscan.properties
 COPY interproscan.properties /usr/local/interproscan-${IPSCAN_VERSION}/interproscan.properties
@@ -20,21 +19,20 @@ RUN tar zxf /tmp/signalp-4.1b.Linux.tar.Z -C /usr/local/interproscan-${IPSCAN_VE
 
 COPY external/tmhmm-2.0c.Linux.tar.gz /tmp/
 RUN  tar zxf /tmp/tmhmm-2.0c.Linux.tar.gz -C /tmp && \
-     cp /tmp/tmhmm-2.0c/bin/decodeanhmm.Linux_x86_64 /usr/local/interproscan-${IPSCAN_VERSION}/bin/tmhmm/2.0c/decodeanhmm
-
+  cp /tmp/tmhmm-2.0c/bin/decodeanhmm.Linux_x86_64 /usr/local/interproscan-${IPSCAN_VERSION}/bin/tmhmm/2.0c/decodeanhmm
 
 COPY external/phobius101_linux.tar.gz /tmp/
 RUN  tar xzf /tmp/phobius101_linux.tar.gz -C /usr/local/interproscan-${IPSCAN_VERSION}/bin/phobius/1.01 --strip-components 3
 
-RUN chmod -R a+rx /usr/local/interproscan-${IPSCAN_VERSION}/bin/* 
+RUN chmod -R a+rx /usr/local/interproscan-${IPSCAN_VERSION}/bin/*
 
 RUN cd /usr/local/interproscan-${IPSCAN_VERSION}; rm -rf data
 
 FROM biocorecrg/debian-perlbrew-pyenv3-java:buster
 
-ARG IPSCAN_VERSION=5.65-97.0
+ARG IPSCAN_VERSION=5.72-103.0
 
-ENV PATH "/usr/local/interproscan:${PATH}"
+ENV PATH="/usr/local/interproscan:${PATH}"
 
 COPY --from=builder /usr/local/interproscan-${IPSCAN_VERSION} /usr/local/interproscan
 

Dockerfile.open

@@ -1,25 +1,24 @@
 FROM biocorecrg/debian-perlbrew-pyenv3-java:buster AS builder
 
-ARG IPSCAN_VERSION=5.65-97.0
+ARG IPSCAN_VERSION=5.72-103.0
 
 # Install InterPro
+RUN cd /usr/local; curl --retry 3 --fail --silent --show-error --location --remote-name https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${IPSCAN_VERSION}/alt/interproscan-core-${IPSCAN_VERSION}.tar.gz && \
+  curl --retry 3 --fail --silent --show-error --location --remote-name https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${IPSCAN_VERSION}/alt/interproscan-core-${IPSCAN_VERSION}.tar.gz.md5 && \
+  md5sum -c interproscan-core-${IPSCAN_VERSION}.tar.gz.md5
 
-RUN cd /usr/local; curl --retry 3 --fail --silent --show-error --location --remote-name https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${IPSCAN_VERSION}/interproscan-${IPSCAN_VERSION}-64-bit.tar.gz && \
-	curl --retry 3 --fail --silent --show-error --location --remote-name https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${IPSCAN_VERSION}/interproscan-${IPSCAN_VERSION}-64-bit.tar.gz.md5 && \
-	md5sum -c interproscan-${IPSCAN_VERSION}-64-bit.tar.gz.md5
-
-RUN cd /usr/local; tar zxf interproscan-${IPSCAN_VERSION}-64-bit.tar.gz --exclude "interproscan-${IPSCAN_VERSION}/data" && rm interproscan-${IPSCAN_VERSION}-64-bit.tar.gz interproscan-${IPSCAN_VERSION}-64-bit.tar.gz.md5
+RUN cd /usr/local; tar zxf interproscan-core-${IPSCAN_VERSION}.tar.gz --exclude "interproscan-${IPSCAN_VERSION}/data" && rm interproscan-core-${IPSCAN_VERSION}.tar.gz interproscan-core-${IPSCAN_VERSION}.tar.gz.md5
 
 # Replace interproscan.properties
 COPY interproscan.properties /usr/local/interproscan-${IPSCAN_VERSION}/interproscan.properties
 RUN chmod a+r /usr/local/interproscan-${IPSCAN_VERSION}/interproscan.properties
-RUN chmod -R a+rx /usr/local/interproscan-${IPSCAN_VERSION}/bin/* 
+RUN chmod -R a+rx /usr/local/interproscan-${IPSCAN_VERSION}/bin/*
 
 RUN cd /usr/local/interproscan-${IPSCAN_VERSION}; rm -rf data
 
 FROM biocorecrg/debian-perlbrew-pyenv3-java:buster
 
-ARG IPSCAN_VERSION=5.65-97.0
+ARG IPSCAN_VERSION=5.72-103.0
 
 ENV PATH "/usr/local/interproscan:${PATH}"
 

README.md

@@ -4,46 +4,44 @@
 
 Container recipes for building [Interproscan](https://interproscan-docs.readthedocs.io) (for [Docker](https://www.docker.com/) and [Singularity](https://singularity.hpcng.org/)).
 
-* If you want to use Interproscan external privative software, these programs must be obtained first with granted academic permissions.
-    * [SignalP](http://www.cbs.dtu.dk/services/SignalP/) ```signalp-4.1b.Linux.tar.Z```
-    * [TMHMM](http://www.cbs.dtu.dk/services/TMHMM/) ```tmhmm-2.0c.Linux.tar.gz```
-    * [Phobious](https://phobius.sbc.su.se/) ```phobius101_linux.tar.gz```
-        * Regarding phobius: https://www.biostars.org/p/238642/
-    * Keep in mind that some other modifications are also needed in those programs above in advance, e. g., replacing ```/usr/bin/perl``` for ```/usr/bin/env perl```
+- If you want to use Interproscan external privative software, these programs must be obtained first with granted academic permissions.
+  - [SignalP](http://www.cbs.dtu.dk/services/SignalP/) `signalp-4.1b.Linux.tar.Z`
+  - [TMHMM](http://www.cbs.dtu.dk/services/TMHMM/) `tmhmm-2.0c.Linux.tar.gz`
+  - [Phobious](https://phobius.sbc.su.se/) `phobius101_linux.tar.gz`
+    - Regarding phobius: https://www.biostars.org/p/238642/
+  - Keep in mind that some other modifications are also needed in those programs above in advance, e. g., replacing `/usr/bin/perl` for `/usr/bin/env perl`
 
 Last software package versions of Interproscan include the whole data by default. For container performance and distribution, we don't keep Interproscan data directory.
 
-It is important to ensure that program and data versions match and that this is adequately reflected in ```interproscan.properties``` or ```interproscan.open.properties``` files. Otherwise Interproscan is not likely to work.
-
 ## Pregenerated images
 
-* [Singularity](https://biocore.crg.eu/iprscan/)
-* [Docker](https://hub.docker.com/r/biocorecrg/interproscan)
+- [Singularity](https://biocore.crg.eu/iprscan/)
+- [Docker](https://hub.docker.com/r/biocorecrg/interproscan)
 
 ## Building from Docker recipes
 
     # With privative software
-    docker build -t iprscan:5.56-89.0 -f Dockerfile .
-    sudo singularity build iprscan-5.56-89.0.sif docker-daemon://iprscan:5.56-89.0
+    docker build -t iprscan:5.72-103.0 -f Dockerfile .
+    sudo singularity build iprscan-5.72-103.0.sif docker-daemon://iprscan:5.72-103.0
     # Without privative software
-    docker build -t iprscan-open:5.56-89.0 -f Dockerfile.open .
-    sudo singularity build iprscan-5.56-89.0.open.sif docker-daemon://iprscan-open:5.56-89.0
+    docker build -t iprscan-open:5.72-103.0 -f Dockerfile.open .
+    sudo singularity build iprscan-5.72-103.0.open.sif docker-daemon://iprscan-open:5.72-103.0
 
-You can avoid using ```sudo``` with ```--fakeroot``` Singularity build option.
+You can avoid using `sudo` with `--fakeroot` Singularity build option.
 
 ## Running
 
 For running the container images, it is mandatory to mount a data directory that fits the same Interproscan version. Below some example commands:
 
 ```
 # Docker
-docker run --volume /path/to/data:/usr/local/interproscan/data --volume /path/to/scratch:/scratch -t biocorecrg/interproscan:5.56-89.0 /usr/local/interproscan/interproscan.sh -i /scratch/test.fa --goterms --iprlookup --pathways -o /scratch/out_interpro -f TSV
+docker run --volume /path/to/data:/usr/local/interproscan/data --volume /path/to/scratch:/scratch -t biocorecrg/interproscan:5.72-103.0 /usr/local/interproscan/interproscan.sh -i /scratch/test.fa --goterms --iprlookup --pathways -o /scratch/out_interpro -f TSV
 
 # Singularity
-singularity exec -B /path/to/data:/usr/local/interproscan/data -e iprscan-5.56-89.0.open.sif /usr/local/interproscan/interproscan.sh -i /path/to/test2.fa --goterms --iprlookup --pathways -o /path/to/out_interpro -f TSV
+singularity exec -B /path/to/data:/usr/local/interproscan/data -e iprscan-5.72-103.0.open.sif /usr/local/interproscan/interproscan.sh -i /path/to/test2.fa --goterms --iprlookup --pathways -o /path/to/out_interpro -f TSV
 ```
 
 ## NOTES
 
-* Moreover, keep into account that a user with suitable permissions may need first to index ```/usr/local/interproscan/data``` directory (e.g., with ```python3 /usr/local/interproscan/initial_setup.py```). You can use the very container images. Details here: https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html
-* Depending on your setup, you may need to change ```SINGULARITY_TMPDIR``` (and ```SINGULARITY_CACHEDIR```) environment variables for pointing to a location with enough space. More details at: https://singularity.hpcng.org/admin-docs/master/installation.html
+- Moreover, keep into account that a user with suitable permissions may need first to index `/usr/local/interproscan/data` directory (e.g., with `python3 /usr/local/interproscan/initial_setup.py`). You can use the very container images. Details here: https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html
+- Depending on your setup, you may need to change `SINGULARITY_TMPDIR` (and `SINGULARITY_CACHEDIR`) environment variables for pointing to a location with enough space. More details at: https://singularity.hpcng.org/admin-docs/master/installation.html

interproscan.properties

@@ -14,18 +14,17 @@ perl.command=perl
 python3.command=python3
 
 # Binary file locations (required for setup.py)
-binary.hmmer3.path=${bin.directory}/hmmer/hmmer3/3.1b1
-binary.hmmer33.path=${bin.directory}/hmmer/hmmer3/3.3
+binary.hmmer3.path=${bin.directory}/hmmer/hmmer3/3.3
 
 ####################################
 # Member databases HMMs
 ####################################
 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=${data.directory}/hamap/2023_01/hamap.hmm.lib
-ncbifam.hmm.path=${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
+hamap.hmm.path=${data.directory}/hamap/2023_05/hamap.hmm.lib
+ncbifam.hmm.path=${data.directory}/ncbifam/15.0/ncbifam.hmm
+panther.hmm.path=${data.directory}/panther/19.0/famhmm/binHmm
+pfam-a.hmm.path=${data.directory}/pfam/37.1/pfam_a.hmm
 pirsf.sfhmm.path=${data.directory}/pirsf/3.10/sf_hmm_all
 pirsr.srhmm.path=${data.directory}/pirsr/2023_05/sr_hmm_all
 sfld.hmm.path=${data.directory}/sfld/4/sfld.hmm