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NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
GNU General Public License v3.0
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Failed execution on Singularity #500

Open jyw-atgithub opened 2 months ago

jyw-atgithub commented 2 months ago

Hi! I am using the singularity on school's computation cluster. After building the sif image of AGAT-1.4.1, I had an error. The processes is shown below:

$module load singularity/3.11.3
$singularity pull docker://quay.io/biocontainers/agat:1.4.1--pl5321hdfd78af_0
$singularity run /pub/jenyuw/Software/agat_1.4.1--pl5321hdfd78af_0.sif
Singularity> agat_convert_sp_gxf2gxf.pl --help
ListUtil.c: loadable library and perl binaries are mismatched (got handshake key 0xcd00080, needed 0xed00080)

In addition, I had tried installation thorugh conda, micromamba, and manual way but all failed. I tried our systems perl modules and both failed. For example I used module load perl/5.30.0 R/4.3.3 (or perl/5.34.1) and both gave me the following message during the make test step. No error messaged at the dependency installation or the make stage. 

Failed 1/8 test programs. 1/254 subtests failed.
make: *** [Makefile:1728: test_dynamic] Error 255

Please tell me if I need to provide more info. Thank you!

Juke34 commented 1 week ago

Sounds there is a conflict between perl coming via the container and some stuff you have on your computer. By default Singu bind/mount some directories from your computer (see the list here https://mivegec.pages.ird.fr/dainat/malbec-containers/pages/containers/containers-7-singularity/#binding-directories). You may have a PERL5LIB environment variable setup somewhere that breaks the path to the singu perl. You should try to check the PERL5LIB (and other specific PERL variable): echo $PERL5LIB Check the perl you are using which perl