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Update InterProScan version from 5.59-91.0 to 5.73-104.0
As of March 2025, the latest version of InterProScan on Bioconda is 5.59_91, which is from October 17, 2022. This PR builds a new version of InterProScan and uses the test data from EBI-Metagenomics' InterProScan module and their Docker image
PR checklist
Closes #XXX
- [ ] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] If you've added a new tool - have you followed the module conventions in the contribution docs
- [ ] If necessary, include test data in your PR.
- [ ] Remove all TODO statements.
- [ ] Emit the
versions.ymlfile. - [ ] Follow the naming conventions.
- [ ] Follow the parameters requirements.
- [ ] Follow the input/output options guidelines.
- [ ] Add a resource
label - [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
- Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
- For modules:
- [ ]
nf-core modules test <MODULE> --profile docker - [ ]
nf-core modules test <MODULE> --profile singularity - [ ]
nf-core modules test <MODULE> --profile conda
- [ ]
- For subworkflows:
- [ ]
nf-core subworkflows test <SUBWORKFLOW> --profile docker - [ ]
nf-core subworkflows test <SUBWORKFLOW> --profile singularity - [ ]
nf-core subworkflows test <SUBWORKFLOW> --profile conda
- [ ]
- For modules:
Getting this docker build error, probably due to an architecture issue
(nf-core-v2)
✘ Mon 24 Mar - 16:15 ~/code/nf-core/modules/modules/nf-core/interproscan origin ☊ master 3☀ 2●
docker build . -t quay.io/nf-core/interproscan:5.73-104.0
[+] Building 23.9s (10/12) docker:desktop-linux
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 1.94kB 0.0s
=> [internal] load metadata for docker.io/mambaorg/micromamba:2.0.5 0.4s
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [internal] load build context 0.0s
=> => transferring context: 9.72kB 0.0s
=> [1/8] FROM docker.io/mambaorg/micromamba:2.0.5@sha256:8d0d4cad074afe3ac93b58dce88bd2659153d3fa6de3a6968f501710e8d3c832 1.6s
=> => resolve docker.io/mambaorg/micromamba:2.0.5@sha256:8d0d4cad074afe3ac93b58dce88bd2659153d3fa6de3a6968f501710e8d3c832 0.0s
=> => sha256:ca8feed3070834bddfa15ffdc519c000852c511f2682af29fd9dfa6fe72d926d 5.86kB / 5.86kB 0.0s
=> => sha256:0996a45dbf081690ef07d06d966daaf33ddccd439dcfe9092dec0cd7bf53e768 122.68kB / 122.68kB 0.5s
=> => sha256:c24f4d9717cc8ead02156bf9ead4a0943dfe7cbf84cb9f4a6b08600f1e263c5b 548B / 548B 0.3s
=> => sha256:8d0d4cad074afe3ac93b58dce88bd2659153d3fa6de3a6968f501710e8d3c832 2.36kB / 2.36kB 0.0s
=> => sha256:7c1325c9891758c8fbb14afa52f5c75ac38c12c9bf0ba8b8d9a37118480284fb 2.18kB / 2.18kB 0.0s
=> => sha256:8d442fcb0ca8120ef7c558109e962bc23e5b9991714a43d11f1255981a5c91ec 8.38MB / 8.38MB 1.0s
=> => sha256:c14b2f689c1b34cb8d9f268f7db19a54408a5a57c01ff7b6a4e57c65765c792c 283B / 283B 0.5s
=> => sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 32B / 32B 0.7s
=> => sha256:bd1693c48ea5c20426b078e87b857fdc684a0973f0a6baae2ce010f6f6003b13 3.79kB / 3.79kB 0.9s
=> => sha256:ad9621110251bbf75f24aaa0c4b52e0802d11bc590921015401adda364b78b19 681B / 681B 1.1s
=> => sha256:a69ca0ecce5760df4d789643fca9750fb31a934c16d235cb32df678cb49124a4 644B / 644B 1.3s
=> => extracting sha256:8d442fcb0ca8120ef7c558109e962bc23e5b9991714a43d11f1255981a5c91ec 0.1s
=> => extracting sha256:0996a45dbf081690ef07d06d966daaf33ddccd439dcfe9092dec0cd7bf53e768 0.0s
=> => extracting sha256:c24f4d9717cc8ead02156bf9ead4a0943dfe7cbf84cb9f4a6b08600f1e263c5b 0.0s
=> => extracting sha256:c14b2f689c1b34cb8d9f268f7db19a54408a5a57c01ff7b6a4e57c65765c792c 0.0s
=> => extracting sha256:bd1693c48ea5c20426b078e87b857fdc684a0973f0a6baae2ce010f6f6003b13 0.0s
=> => sha256:5b30bfc33ca93fed51a26f6dedad278c650faf9eb6ddc752796d4e31cb4c10b1 343B / 343B 1.5s
=> => extracting sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 0.0s
=> => extracting sha256:ad9621110251bbf75f24aaa0c4b52e0802d11bc590921015401adda364b78b19 0.0s
=> => extracting sha256:a69ca0ecce5760df4d789643fca9750fb31a934c16d235cb32df678cb49124a4 0.0s
=> => extracting sha256:5b30bfc33ca93fed51a26f6dedad278c650faf9eb6ddc752796d4e31cb4c10b1 0.0s
=> [2/8] COPY --chown=mambauser:mambauser env.lock /tmp/env.lock 0.0s
=> [3/8] RUN micromamba install --name base --yes --file /tmp/env.lock && micromamba clean --all --yes 19.8s
=> [4/8] RUN apt-get update && apt-get install -y --no-install-recommends libgomp1 && rm -rf /var/lib/apt/lists/* 2.2s
=> [5/8] WORKDIR /opt 0.0s
=> ERROR [6/8] RUN wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.73-104.0/alt/interproscan-core-5.73-104.0.tar.gz && wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.73-104. 0.1s
------
> [6/8] RUN wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.73-104.0/alt/interproscan-core-5.73-104.0.tar.gz && wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.73-104.0/alt/interproscan-core-5.73-104.0.tar.gz.md5 && md5sum -c interproscan-core-5.73-104.0.tar.gz.md5 && tar -zxf interproscan-core-5.73-104.0.tar.gz && rm interproscan-core-5.73-104.0.tar.gz* && mv /opt/interproscan-5.73-104.0 /opt/interproscan:
0.106 qemu-x86_64: Could not open '/lib64/ld-linux-x86-64.so.2': No such file or directory
------
Dockerfile:29
--------------------
28 |
29 | >>> RUN wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${VERSION}/alt/interproscan-core-${VERSION}.tar.gz && \
30 | >>> wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${VERSION}/alt/interproscan-core-${VERSION}.tar.gz.md5 && \
31 | >>> md5sum -c interproscan-core-${VERSION}.tar.gz.md5 && \
32 | >>> tar -zxf interproscan-core-${VERSION}.tar.gz && \
33 | >>> rm interproscan-core-${VERSION}.tar.gz* && \
34 | >>> mv /opt/interproscan-${VERSION} /opt/interproscan
35 |
--------------------
ERROR: failed to solve: process "/usr/local/bin/_dockerfile_shell.sh wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${VERSION}/alt/interproscan-core-${VERSION}.tar.gz && wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${VERSION}/alt/interproscan-core-${VERSION}.tar.gz.md5 && md5sum -c interproscan-core-${VERSION}.tar.gz.md5 && tar -zxf interproscan-core-${VERSION}.tar.gz && rm interproscan-core-${VERSION}.tar.gz* && mv /opt/interproscan-${VERSION} /opt/interproscan" did not complete successfully: exit code: 255
Linting is failing due to a known edge case in nf-core/tools: https://github.com/nf-core/modules/pull/7106
But more importantly, the docker test is failing 😭. I'm seeing the error is happening because of error 193, which maybe a code dump? But most of the evidence I can find is from Windows-specific machines, which doesn't apply here.
- https://github.com/moby/moby/issues/22473
- https://stackoverflow.com/questions/2229247/gdb-fails-with-error-193-when-debugging-mingw-compiled-code
- https://www.sysnative.com/forums/threads/dism-online-error-193.18939/
Test Process INTERPROSCAN
Test [9558abd4] 'test_interproscan'
> Nextflow 24.10.5 is available - Please consider updating your version to it
> N E X T F L O W ~ version 24.10.2
> Launching `/home/runner/_work/modules/modules/.nf-test-9558abd4d63711d51a9f6c34f816dea.nf` [focused_cray] DSL2 - revision: 4dce7f2d26
> [2c/80aeab] Submitted process > INTERPROSCAN (test)
> ERROR ~ Error executing process > 'INTERPROSCAN (test)'
>
> Caused by:
> Process `INTERPROSCAN (test)` terminated with an error exit status (137)
>
>
> Command executed:
>
> interproscan.sh \
> -cpu 2 \
> -i test.fasta \
> -dp \
> -appl Coils \
> --output-file-base test
>
> gzip test.{tsv,xml,gff3,json}
>
> cat <<-END_VERSIONS > versions.yml
> "INTERPROSCAN":
> InterProScan: $(interproscan.sh --version | grep -o "InterProScan version [0-9.-]*" | sed "s/InterProScan version //")
> InterProScan database: 5.73-104.0
> END_VERSIONS
>
> Command exit status:
> 137
>
> Command output:
> 26/03/2025 22:02:57:720 Welcome to InterProScan-5.73-104.0
> 26/03/2025 22:02:57:721 Running InterProScan v5 in STANDALONE mode... on Linux
> 26/03/2025 22:03:01:304 RunID: a52681ec4365_20250326_220301155_ft8w
>
> Command error:
> a1349eb17b3c: Waiting
> 0f2c86814122: Waiting
> f9c0d12f2d56: Waiting
> d143f88ecec4: Verifying Checksum
> d143f88ecec4: Download complete
> abe470f33e5d: Download complete
> c14b2f689c1b: Verifying Checksum
> c14b2f689c1b: Download complete
> 6441b907fc72: Verifying Checksum
> 6441b907fc72: Download complete
> bd9ddc54bea9: Verifying Checksum
> bd9ddc54bea9: Download complete
> c24f4d9717cc: Verifying Checksum
> c24f4d9717cc: Download complete
> 84bb1dd1d3f6: Verifying Checksum
> 84bb1dd1d3f6: Download complete
> 7c86c8ee49bb: Download complete
> 849cd77bc683: Verifying Checksum
> 849cd77bc683: Download complete
> a1349eb17b3c: Verifying Checksum
> a1349eb17b3c: Download complete
> 6c693a08874e: Verifying Checksum
> 6c693a08874e: Download complete
> d2eb42b4a5eb: Download complete
> 0f2c86814122: Download complete
> d2eb42b4a5eb: Pull complete
> d143f88ecec4: Pull complete
> abe470f33e5d: Pull complete
> c24f4d9717cc: Pull complete
> c14b2f689c1b: Pull complete
> 6441b907fc72: Pull complete
> bd9ddc54bea9: Pull complete
> 849cd77bc683: Pull complete
> 84bb1dd1d3f6: Pull complete
> 7c86c8ee49bb: Pull complete
> a1349eb17b3c: Pull complete
> ec[591](https://github.com/nf-core/modules/actions/runs/14094253854/job/39478263031?pr=8003#step:6:611)27ced78: Verifying Checksum
> ec59127ced78: Download complete
> f9c0d12f2d56: Verifying Checksum
> f9c0d12f2d56: Download complete
> f9c0d12f2d56: Pull complete
> 6c693a08874e: Pull complete
> ec59127ced78: Pull complete
> 0f2c86814122: Pull complete
> Digest: sha256:71ea3640969ee7aa8bfc33baf942b55e7123552[593](https://github.com/nf-core/modules/actions/runs/14094253854/job/39478263031?pr=8003#step:6:613)5697f6498ec2b60490bc2e
> Status: Downloaded newer image for quay.io/nf-core/interproscan:5.73-104.0
> 26/03/2025 22:02:57:720 Welcome to InterProScan-5.73-104.0
> 26/03/2025 22:02:57:721 Running InterProScan v5 in STANDALONE mode... on Linux
> 26/03/2025 22:03:01:304 RunID: a52681ec4365_20250326_220301155_ft8w
> /opt/interproscan/interproscan.sh: line 56: 193 Killed "$JAVA" -XX:ParallelGCThreads=8 -Xms2028M -Xmx9216M $PROPERTY -jar interproscan-5.jar $@ -u $USER_DIR
>
> Work dir:
> /home/runner/_work/modules/modules/.nf-test/tests/9558abd4d63711d51a9f6c34f816dea/work/2c/80aeabd9e8f352a4faa9a6371fa53b
>
> Container:
> quay.io/nf-core/interproscan:5.73-104.0
>
> Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
>
> -- Check '/home/runner/_work/modules/modules/.nf-test/tests/9558abd4d63711d51a9f6c34f816dea/meta/nextflow.log' file for details