Another shared library error

[ehj000]

Samtools flag_filter fails with the following error: samtools: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory. The tools is part of a workflow for the IBA course

[kjetilkl]

This error applies to the "samtools:1.2" container and also "samtools:0.1.18", but the other versions available on our production server work fine (v0.1.19, 1.3.1, 1.8 and 1.9).

I tried to delete the container and rebuild it, but the result was the same. I also tried to add the two dependencies "ncurses==5.9" and "zlib==1.2.8" as requirements in the tool wrapper itself in order to create a new mulled container, but no container was created. A possible solution could be to change the tool requirement from samtools 1.2 to samtools 1.3, since the latter container works.

[torfinnnome]

Did you restart Galaxy after modifying the tool wrapper xml file?

man. 9. aug. 2021 kl. 16:35 skrev Kjetil Klepper @.***>:

This error applies to the "samtools:1.2" container and also "samtools:0.1.18", but the other versions available on our production server work fine (v0.1.19, 1.3.1, 1.8 and 1.9).

I tried to delete the container and rebuild it, but the result was the same. I also tried to add the two dependencies "ncurses==5.9" and "zlib==1.2.8" as requirements in the tool wrapper itself in order to create a new mulled container, but no container was created. A possible solution could be to change the tool requirement from samtools 1.2 to samtools 1.3, since the latter container works.

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[kjetilkl]

I forgot to restart Galaxy, but it wasn't necessary. The attempt to build the mulled container fails.

SOUT Collecting package metadata (current_repodata.json): ...working... done
SOUT Solving environment: ...working... done
SOUT ## Package Plan ##
SOUT environment location: /usr/local
SOUT added / updated specs:
SOUT - ncurses=5.9
SOUT - samtools=1.2
SOUT - zlib=1.2.8
SOUT The following packages will be downloaded:
SOUT package                    |            build
SOUT ---------------------------|-----------------
SOUT ncurses-5.9                |               10         1.1 MB  conda-forge
SOUT samtools-1.2               |                2         1.3 MB  bioconda
SOUT zlib-1.2.8                 |                3          87 KB  conda-forge
SOUT ------------------------------------------------------------
SOUT Total:         2.4 MB
SOUT The following NEW packages will be INSTALLED:
SOUT ncurses            conda-forge/linux-64::ncurses-5.9-10
SOUT samtools           bioconda/linux-64::samtools-1.2-2
SOUT zlib               conda-forge/linux-64::zlib-1.2.8-3
SOUT Preparing transaction: ...working... done
SOUT Verifying transaction: ...working... done
SOUT Executing transaction: ...working... done
[10/Aug/2021:10:43:01 +0200] "GET /api/histories/06d5df884b950ef5/contents?details=cb3b5ab54becca5e%2Cb142f3f7bda895cf&order
req: 20/68] 82.164.29.235 () {58 vars in 1436 bytes} [Tue Aug 10 10:43:01 2021] GET /api/histories/06d5df884b950ef5/contents
DEBU Container [f516c4b88ae2 step-0450d2e026] completed with exit code [0] as expected
DEBU Container [f516c4b88ae2 step-0450d2e026] removed
STEP Wrap [build/dist] as [quay.io/biocontainers/mulled-v2-f52cdfd19068e9297c284d2ff5cd659fd68e1f6d:be932bda8d37499f0d7da2b9
DEBU Creating container [step-5a8fc26366]
DEBU Packing succeeded
INFO Invoke Task [singularity]
STEP Run image [quay.io/biocontainers/singularity:2.4.6--0] with command [[mkdir -p /usr/local/var/singularity/mnt/container
DEBU Creating container [step-63c8033efc]
DEBU Created container [128d0657b127 step-63c8033efc], starting it
DEBU Container [128d0657b127 step-63c8033efc] started, waiting for completion
SOUT Using container recipe deffile: /import/Singularity.def
SOUT Sanitizing environment
SOUT Adding base Singularity environment to container
[10/Aug/2021:10:43:06 +0200] "GET /api/histories/06d5df884b950ef5/contents?details=cb3b5ab54becca5e%2Cb142f3f7bda895cf&order
req: 21/69] 82.164.29.235 () {58 vars in 1436 bytes} [Tue Aug 10 10:43:06 2021] GET /api/histories/06d5df884b950ef5/contents
SOUT Docker image path: quay.io/bioconda/base-glibc-busybox-bash:latest
SOUT Cache folder set to /root/.singularity/docker

SOUT Exploding layer: sha256:c1a16a04cedd950c541fa85e64b62b17eb3b73a7f7e29ea3db23dc9b83dfcade.tar.gz
SOUT Exploding layer: sha256:4ca545ee6d5db5c1170386eeb39b2ffe3bd46e5d4a73a9acbebc805f19607eb3.tar.gz
SOUT Exploding layer: sha256:9771adeedf210aa0eb530f7eb2eeb5b1a9537ba1868355b470cddafd884b91c5.tar.gz
SERR + echo Copying conda environment
SERR + mkdir -p /tmp/conda
SOUT Copying conda environment
SERR + cp -r /data/dist/bin /data/dist/conda-meta /data/dist/include /data/dist/lib /data/dist/share /tmp/conda/
SOUT Running post scriptlet
SERR + rm -R /usr/local
SERR + mkdir -p /usr/local
SERR + cp -R /tmp/conda/bin /tmp/conda/conda-meta /tmp/conda/include /tmp/conda/lib /tmp/conda/share /usr/local/
SOUT Running test scriptlet
SERR + true
SOUT Finalizing Singularity container
SOUT Calculating final size for metadata...
SOUT Skipping checks
SOUT Building Singularity image...
SERR mksquashfs: error while loading shared libraries: /usr/lib/x86_64-linux-gnu/liblz4.so.1: invalid ELF header
SERR ERROR: Failed squashing image, left template directory at: /tmp/.singularity-build.lZitAx

[torfinnnome]

@ehj000 "samtools flag_filter" is an old tool (2016, no updates, by a user brennic). Would it be possible to modify your workflow to use the IUC tool "samtools view", which should provide the same results?

[ehj000]

I will try to replace the old tool and report back

[ehj000]

I am able to use samtools view instead. Thanks

[torfinnnome]

Should we remove this tool "Samtools flag_filter", perhaps?

[ehj000]

Yes, I can clean up the old tools that were installed with the AmrPlusPlus pipeline