Issue with RNAFramework installation

[Frappadoo]

Hi Danny,

I have recently tried to install RNAFramework on a CentOS, however, I can't seem to get it to run, as every time I try to run it, it gives me the following error.

-bash: rf-map: command not found

Do you have any suggestions on how to solve this?

Thank you,

Fran

[dincarnato]

Hi Fran,

it looks like you haven't added the RNAFramework install dir to your PATH.

Best, Danny

[Frappadoo]

Hi Danny,

I have forgot to mention that I have added it to my bashrc file and sourced it. And it is still resulting in that error.

Best wishes,

Fran

———————————— Francesca Appadoo (pronouns she, her) BSc (Hons) MSc PhD student Tuplin group University of Leeds

---

From: Danny Incarnato @.> Sent: Thursday, June 27, 2024 9:58:33 AM To: dincarnato/RNAFramework @.> Cc: Francesca Appadoo @.>; Author @.> Subject: Re: [dincarnato/RNAFramework] Issue with RNAFramework installation (Issue #63)

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Hi Fran,

it looks like you haven't added the RNAFramework install dir to your PATH.

Best, Danny

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[dincarnato]

Francesca,

the error comes from your system, not the RNA Framework. Where is your RNAFramework install dir located? Can you paste here the output of the following command:

echo $PATH

Best, Danny

[Frappadoo]

Hi Danny, this is the output echo $PATH /nobackup/leedsomics_tools/RNAFramework:/nobackup/leedsomics_tools/shapemapper2:/nobackup/leedsomics_tools/RNAFramework:/nobackup/leedsomics_tools/shapemapper2:/nobackup/bsjma_relion4/relion/build/bin/:/apps/mpi/bin:/apps/developers/libraries/openmpi/3.1.4/1/intel-19.0.4/bin:/apps/developers/compilers/intel/19.0.4/1/default/compilers_and_libraries_2019.4.243/linux/bin/intel64:/apps/developers/compilers/intel/19.0.4/1/default/debugger_2019/gdb/intel64/bin:/services/sge_prod/bin/lx-amd64:/services/sge_prod/default/common/leeds/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/apps/bin:/nobackup/leedsomics_tools/RNAFramework/

Best,

Fran

[dincarnato]

I assume RNAFramework is inside /nobackup/leedsomics_tools/RNAFramework/. Can you also do:

ls -l /nobackup/leedsomics_tools/RNAFramework/

[Frappadoo]

Ah got it looks like I don't have permission:

ls -l /nobackup/leedsomics_tools/RNAFramework/ ls: cannot open directory /nobackup/leedsomics_tools/RNAFramework/: Permission denied

[dincarnato]

Great. Feel free to close the issue if solved.

[Frappadoo]

Hi Danny,

I got permission to the files now and have checked that RNAFramework is in my PATH, but it is still giving me the same error.

[dincarnato]

This is an error caused by the way things are configured on your system, non an RNAFramework issue. Your system administrator is the best person to ask for help.

Anyway, can you share the output of the command?

ls -l /nobackup/leedsomics_tools/RNAFramework/

[Frappadoo]

ls -l /nobackup/leedsomics_tools/RNAFramework/ total 744 -rwxr-xr-x 1 fbsev fbs 24726 Jun 7 15:14 CHANGELOG.md -rwxr-xr-x 1 fbsev fbs 372 Jun 7 15:14 index.rst drwxr-xr-x 11 fbsev fbs 4096 Jun 7 15:14 lib -rwxr-xr-x 1 fbsev fbs 35797 Jun 7 15:14 LICENSE -rwxr-xr-x 1 fbsev fbs 2139 Jun 7 15:14 README.md -rwxr-xr-x 1 fbsev fbs 19762 Jun 7 15:14 rf-combine -rwxr-xr-x 1 fbsev fbs 13875 Jun 7 15:14 rf-compare -rwxr-xr-x 1 fbsev fbs 16059 Jun 7 15:14 rf-correlate -rwxr-xr-x 1 fbsev fbs 54987 Jun 7 15:14 rf-count -rwxr-xr-x 1 fbsev fbs 52249 Jun 7 15:14 rf-count-genome -rwxr-xr-x 1 fbsev fbs 56560 Jun 7 15:14 rf-duplex -rwxr-xr-x 1 fbsev fbs 12409 Jun 7 15:14 rf-eval -rwxr-xr-x 1 fbsev fbs 75410 Jun 7 15:14 rf-fold -rwxr-xr-x 1 fbsev fbs 23765 Jun 7 15:14 rf-index -rwxr-xr-x 1 fbsev fbs 16535 Jun 7 15:14 rf-jackknife -rwxr-xr-x 1 fbsev fbs 34942 Jun 7 15:14 rf-json2rc -rwxr-xr-x 1 fbsev fbs 33465 Jun 7 15:14 rf-map -rwxr-xr-x 1 fbsev fbs 14769 Jun 7 15:14 rf-modcall -rwxr-xr-x 1 fbsev fbs 27294 Jun 7 15:14 rf-motifdiscovery -rwxr-xr-x 1 fbsev fbs 37897 Jun 7 15:14 rf-mutate -rwxr-xr-x 1 fbsev fbs 37659 Jun 7 15:14 rf-norm -rwxr-xr-x 1 fbsev fbs 21025 Jun 7 15:14 rf-normfactor -rwxr-xr-x 1 fbsev fbs 36205 Jun 7 15:14 rf-peakcall -rwxr-xr-x 1 fbsev fbs 14882 Jun 7 15:14 rf-rctools -rwxr-xr-x 1 fbsev fbs 20974 Jun 7 15:14 rf-structextract -rwxr-xr-x 1 fbsev fbs 8880 Jun 7 15:14 rf-wiggle drwxr-xr-x 2 fbsev fbs 4096 Jun 7 15:14 tests -rwxr-xr-x 1 fbsev fbs 7 Jun 7 15:14 VERSION

[dincarnato]

If you echo $PATH is the path to RNAFramework still there?

[Frappadoo]

Yes it is still there

[dincarnato]

If you issue this:

/nobackup/leedsomics_tools/RNAFramework/rf-map -h

what does it say?

[Frappadoo]

/nobackup/leedsomics_tools/RNAFramework/rf-map -h : No such file or directory

[dincarnato]

And if you do ls -l /nobackup/leedsomics_tools/RNAFramework/rf-map

[Frappadoo]

ls -l /nobackup/leedsomics_tools/RNAFramework/rf-map-rwxr-xr-x 1 fbsev fbs 33465 Jun 7 15:14 /nobackup/leedsomics_tools/RNAFramework/rf-map

[dincarnato]

Francesca, I am sorry but this is clearly an issue with permissions on your server. The folder is in your path, you can list its content, the files are executable, but apparently you can't execute them, which has nothing to do with RNA Framework. You should contact your server admin and have it fixed.

It is unclear to me how did you manage to clone the git repo, if you could not even list the directory content. My suggestion is to git clone the repo inside your home directory and try again.

Best, Danny

[Frappadoo]

I'll contact the administrator that has installed this and ask to get permission. Thank you for your help