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NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit
GNU General Public License v3.0
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Semi-manual installation of AGAT fails most installation tests #394

Closed pzit0 closed 6 months ago

pzit0 commented 10 months ago

I've tried installing AGAT but the following command prompts a huge error message (shown below, redacted). I've previously tried installing through conda, however, it cannot solve an environment issue, and it keeps going indefinitely. Is there any way to fix this?

(base) pzito@IBIO-DRW7N0JQY0 AGAT % make test Test Summary Report

t/config.t (Wstat: 512 Tests: 3 Failed: 2) Failed tests: 1, 3 Non-zero exit status: 2 t/gff_other.t (Wstat: 1024 Tests: 4 Failed: 4) Failed tests: 1-4 Non-zero exit status: 4 t/gff_syntax.t (Wstat: 11520 Tests: 45 Failed: 45) Failed tests: 1-45 Non-zero exit status: 45 t/gff_version.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: No plan found in TAP output t/level_missing.t (Wstat: 3328 Tests: 13 Failed: 13) Failed tests: 1-13 Non-zero exit status: 13 t/scripts_compile.t (Wstat: 19712 Tests: 77 Failed: 77) Failed tests: 1-77 Non-zero exit status: 77 t/scripts_output.t (Wstat: 20480 Tests: 80 Failed: 80) Failed tests: 1-80 Non-zero exit status: 80 t/unitest.t (Wstat: 512 Tests: 0 Failed: 0) Non-zero exit status: 2 Parse errors: Bad plan. You planned 15 tests but ran 0. Files=8, Tests=222, 20 wallclock secs ( 0.06 usr 0.02 sys + 6.43 cusr 2.32 csys = 8.83 CPU) Result: FAIL Failed 8/8 test programs. 221/222 subtests failed. make: *** [test_dynamic] Error 2

Juke34 commented 10 months ago

When installing via conda, be sure to use a fresh new environment. You can also try with Mamba instead of conda (you will need to install mamba first)

Otherwise, run perl -I lib/ t/gff_other.t to get more details about error when running the gff_other.t test

Maybe you should consider to use a container version

pzit0 commented 10 months ago

Hi!

I've tried on different conda environments, but it doesn't seem to be working for me. Here's the detailed version of the failed tests:

(base) pzito@IBIO-DRW7N0JQY0 AGAT % perl -I lib/ t/gff_other.t 1..4 Can't locate AGAT/AGAT.pm in @INC (you may need to install the AGAT::AGAT module) (@INC contains: /Library/Perl/5.30/darwin-thread-multi-2level /Library/Perl/5.30 /Network/Library/Perl/5.30/darwin-thread-multi-2level /Network/Library/Perl/5.30 /Library/Perl/Updates/5.30.3 /System/Library/Perl/5.30/darwin-thread-multi-2level /System/Library/Perl/5.30 /System/Library/Perl/Extras/5.30/darwin-thread-multi-2level /System/Library/Perl/Extras/5.30) at bin/agat_convert_sp_gxf2gxf.pl line 10. BEGIN failed--compilation aborted at bin/agat_convert_sp_gxf2gxf.pl line 10. diff: tmp.gff: No such file or directory not ok 1 - zip_and_fasta check

Failed test 'zip_and_fasta check'

at t/gff_other.t line 40.

Can't locate AGAT/AppEaser.pm in @INC (you may need to install the AGAT::AppEaser module) (@INC contains: /Library/Perl/5.30/darwin-thread-multi-2level /Library/Perl/5.30 /Network/Library/Perl/5.30/darwin-thread-multi-2level /Network/Library/Perl/5.30 /Library/Perl/Updates/5.30.3 /System/Library/Perl/5.30/darwin-thread-multi-2level /System/Library/Perl/5.30 /System/Library/Perl/Extras/5.30/darwin-thread-multi-2level /System/Library/Perl/Extras/5.30) at bin/agat line 8. BEGIN failed--compilation aborted at bin/agat line 8. Can't locate AGAT/AGAT.pm in @INC (you may need to install the AGAT::AGAT module) (@INC contains: /Library/Perl/5.30/darwin-thread-multi-2level /Library/Perl/5.30 /Network/Library/Perl/5.30/darwin-thread-multi-2level /Network/Library/Perl/5.30 /Library/Perl/Updates/5.30.3 /System/Library/Perl/5.30/darwin-thread-multi-2level /System/Library/Perl/5.30 /System/Library/Perl/Extras/5.30/darwin-thread-multi-2level /System/Library/Perl/Extras/5.30) at bin/agat_convert_sp_gxf2gxf.pl line 10. BEGIN failed--compilation aborted at bin/agat_convert_sp_gxf2gxf.pl line 10. diff: tmp.gff: No such file or directory not ok 2 - tabix check

Failed test 'tabix check'

at t/gff_other.t line 51.

Can't locate AGAT/AGAT.pm in @INC (you may need to install the AGAT::AGAT module) (@INC contains: /Library/Perl/5.30/darwin-thread-multi-2level /Library/Perl/5.30 /Network/Library/Perl/5.30/darwin-thread-multi-2level /Network/Library/Perl/5.30 /Library/Perl/Updates/5.30.3 /System/Library/Perl/5.30/darwin-thread-multi-2level /System/Library/Perl/5.30 /System/Library/Perl/Extras/5.30/darwin-thread-multi-2level /System/Library/Perl/Extras/5.30) at bin/agat_convert_sp_gxf2gxf.pl line 10. BEGIN failed--compilation aborted at bin/agat_convert_sp_gxf2gxf.pl line 10. diff: tmp.gff: No such file or directory not ok 3 - issue329 check

Failed test 'issue329 check'

at t/gff_other.t line 62.

Can't locate AGAT/AGAT.pm in @INC (you may need to install the AGAT::AGAT module) (@INC contains: /Library/Perl/5.30/darwin-thread-multi-2level /Library/Perl/5.30 /Network/Library/Perl/5.30/darwin-thread-multi-2level /Network/Library/Perl/5.30 /Library/Perl/Updates/5.30.3 /System/Library/Perl/5.30/darwin-thread-multi-2level /System/Library/Perl/5.30 /System/Library/Perl/Extras/5.30/darwin-thread-multi-2level /System/Library/Perl/Extras/5.30) at bin/agat_convert_sp_gxf2gxf.pl line 10. BEGIN failed--compilation aborted at bin/agat_convert_sp_gxf2gxf.pl line 10. diff: tmp.gff: No such file or directory not ok 4 - issue368 check

Failed test 'issue368 check'

at t/gff_other.t line 72.

Looks like you failed 4 tests of 4.

Am I missing any prerequisite modules? Or do I have to install AGAT::AGAT module separately?

Thanks! Patricia

Juke34 commented 8 months ago

Instead of conda you can try mamba it is much faster to resolve the env. Otherwise you may prefer to use the container. For the manual installation, only the test throw errors? From what Insee it sounds the test is not run from the correct location. Did you clone the repo and followed the protocol from the readme?