InterProScan/5.33-72.0-intel-2018b

[hughesdj]

Having loaded this module, I must also load Python3 to avoid errors.
https://github.com/ebi-pf-team/interproscan/wiki/InstallationRequirements confirms that Python 3 is required for InterProScan 5.30-69.0 onwards.
Perhaps this has not been picked up in the easyconfig.

[boegel]

@hughesdj Can you give an example of a command that triggers the issue (so we can perhaps use that as a sanity check command to catch the issue in the future)?

[hughesdj]

Thanks Kenneth: Pls see below. Without “module load Python”, I got “missing Python3” errors bash-4.2$ module load InterProScan bash-4.2$ module load Python The following have been reloaded with a version change: 1) GCCcore/7.3.0 => GCCcore/8.2.0 2) GMP/6.1.2-GCCcore-7.3.0 => GMP/6.1.2-GCCcore-8.2.0 3) Python/2.7.14-intel-2018b => Python/3.7.2-GCCcore-8.2.0 4) SQLite/3.20.1-GCCcore-7.3.0 => SQLite/3.27.2-GCCcore-8.2.0 5) Tcl/8.6.7-GCCcore-7.3.0 => Tcl/8.6.9-GCCcore-8.2.0 6) bzip2/1.0.6-GCCcore-7.3.0 => bzip2/1.0.6-GCCcore-8.2.0 7) libffi/3.2.1-GCCcore-7.3.0 => libffi/3.2.1-GCCcore-8.2.0 8) libreadline/7.0-GCCcore-7.3.0 => libreadline/8.0-GCCcore-8.2.0 9) ncurses/6.0-GCCcore-7.3.0 => ncurses/6.1-GCCcore-8.2.0 10) zlib/1.2.11-GCCcore-7.3.0 => zlib/1.2.11-GCCcore-8.2.0 bash-4.2$ module list Currently Loaded Modules: 1) Java/1.8.0_162 9) libjpeg-turbo/2.0.0-GCCcore-7.3.0 17) Tcl/8.6.9-GCCcore-8.2.0 2) expat/2.2.5-GCCcore-7.3.0 10) libgd/2.2.5-GCCcore-7.3.0 18) SQLite/3.27.2-GCCcore-8.2.0 3) Perl/5.28.0-GCCcore-7.3.0 11) InterProScan/5.33-72.0-intel-2018b 19) XZ/5.2.4-GCCcore-8.2.0 4) libpng/1.6.34-GCCcore-7.3.0 12) GCCcore/8.2.0 20) GMP/6.1.2-GCCcore-8.2.0 5) freetype/2.9.1-GCCcore-7.3.0 13) bzip2/1.0.6-GCCcore-8.2.0 21) libffi/3.2.1-GCCcore-8.2.0 6) util-linux/2.32-GCCcore-7.3.0 14) zlib/1.2.11-GCCcore-8.2.0 22) Python/3.7.2-GCCcore-8.2.0 7) fontconfig/2.13.0-GCCcore-7.3.0 15) ncurses/6.1-GCCcore-8.2.0 8) NASM/2.13.03-GCCcore-7.3.0 16) libreadline/8.0-GCCcore-8.2.0 bash-4.2$ interproscan.sh -i test_proteins.fasta -f tsv #test_proteins.fasta comes with the distribution (https://github.com/ebi-pf-team/interproscan/wiki/HowToRun)

[hughesdj]

Do you need anything more from me?

[boegel]

@hughesdj I just realized that InterProScan-5.33-72.0-intel-2018b.eb is not included in the central easyconfigs repository yet...

Where did you get this easyconfig file from?

The most recent InterProScan version we have an easyconfig file for in the central repo is 5.28-67.0, so there the system Python 2 is probably providing the necessary dependency (which is still an issue, installed software shouldn't rely on the system Python).

[hughesdj]

Our previous SysAdmin installed it, but he has now left. I regret I don’t know where he found it. We would be grateful for a more recent easyconfig for InterProScan. From: Kenneth Hoste <notifications@github.com> Sent: 12 October 2019 16:38 To: easybuilders/easybuild-easyconfigs <easybuild-easyconfigs@noreply.github.com> Cc: David Hughes <david.hughes@rothamsted.ac.uk>; Mention <mention@noreply.github.com> Subject: Re: [easybuilders/easybuild-easyconfigs] InterProScan/5.33-72.0-intel-2018b (#9043) @hughesdj<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fhughesdj&data=01%7C01%7Cdavid.hughes%40rothamsted.ac.uk%7C256856ff5e0f4177e6df08d74f2a1b23%7Cb688362589414342b0e37b8cc8392f64%7C1&sdata=fSFiJIjxhdgi3Ho0dyGsTS7hurM%2FQoEMCvhkiTF90ks%3D&reserved=0> I just realized that InterProScan-5.33-72.0-intel-2018b.eb is not included in the central easyconfigs repository yet... Where did you get this easyconfig file from? The most recent InterProScan version we have an easyconfig file for in the central repo is 5.28-67.0, so there the system Python 2 is probably providing the necessary dependency (which is still an issue, installed software shouldn't rely on the system Python). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Feasybuilders%2Feasybuild-easyconfigs%2Fissues%2F9043%3Femail_source%3Dnotifications%26email_token%3DABDYPIK4UPJS6HB6KCRK5C3QOHVL3A5CNFSM4I4GUA6KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBCCCDA%23issuecomment-541335820&data=01%7C01%7Cdavid.hughes%40rothamsted.ac.uk%7C256856ff5e0f4177e6df08d74f2a1b23%7Cb688362589414342b0e37b8cc8392f64%7C1&sdata=9HsWPrIZ5aXerAHrW%2F2wsk1QSgQvW1iu%2FrVVnHRkv7s%3D&reserved=0>, or unsubscribe<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FABDYPILRCVMIZKWDQUAVA3LQOHVL3ANCNFSM4I4GUA6A&data=01%7C01%7Cdavid.hughes%40rothamsted.ac.uk%7C256856ff5e0f4177e6df08d74f2a1b23%7Cb688362589414342b0e37b8cc8392f64%7C1&sdata=2uiFnWsWhT99lWkpz9THrUYM16johg9y9LJxV8U1Ygc%3D&reserved=0>. Rothamsted Research is a company limited by guarantee, registered in England at Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a not for profit charity number 802038.