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medvedevgroup / SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs
http://medvedevgroup.com/
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time should be conda dependency #23

Open cjfiscus opened 3 years ago

cjfiscus commented 3 years ago

Hi,

Installed sibeliaz from conda on linux centOS system. Attempted to run with test dataset and receive the following output:

Constructing the graph... line 131: /usr/bin/time: No such file or directory line 132: /usr/bin/time: No such file or directory rm: cannot remove './sibeliaz_test/de_bruijn_graph.dbg': No such file or directory line 137: /usr/bin/time: No such file or directory

I am running on a shared cluster and therefore do not have permission to install time in /usr/bin. time is installed on the system elsewhere and I updated these lines in the sibeliaz script to reflect the path to installed time.

Then when I run I get -f: command not found

My guess is that the version of time that is installed is too old and does not have the -f flag.

Then I installed time from conda (https://anaconda.org/conda-forge/time) and changed the path to time in the sibeliaz file to the time installed by conda and the script works.

Would it be possible to add time as conda dependency and update the sibeliaz script to rely on the version of time installed by conda?

iminkin commented 3 years ago

Hi, thank you for reporting the issue and sorry for the late reply. You can safely remove time from the script, it is just a remnant from the initial version. I will likely remove time in the next release.

smallfade commented 3 years ago

Any possible workaround to work on a cluster and without building the source?

iminkin commented 3 years ago

Any possible workaround to work on a cluster and without building the source?

I think I can just make a small release this week, it will also incorporate the fix for #21

smallfade commented 3 years ago

Any possible workaround to work on a cluster and without building the source?

I think I can just make a small release this week, it will also incorporate the fix for #21

That would be of great help! Thanks!

iminkin commented 3 years ago

Hi @smallfade,

SibeliaZ 1.2.3 that does not depend on time should be in bioconda now.