Comments (9)
Hi Narges,
It doesn't look like the new release has made it to conda yet (I don't know what the schedule for that is). So you will need to clone this repo using git:
git clone https://github.com/SionBayliss/PIRATE.git
And then point to the local files for PIRATE to run commands:
/path/to/local/directory/PIRATE -i input -o output etc....
All the best,
Sion
from pirate.
Hi Narges,
What method are you using for installation and onto which operating system? I would recommend Conda if at all possible. Is the feedback in your comment from the tests run as a part of the installation via conda or have you run --test separately?
All the best,
Sion
from pirate.
Hi Sion
Thank you for your reply.
I am trying to install PIRATE on Linux server, using conda. I also tried "conda install -c sionbayliss pirate".
The report is from "PIRATE --check".
(pirate-env) [narges@node1982 ~]$ PIRATE --check
Running PIRATE on test files:
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:
Tange, O. (2022, May 22). GNU Parallel 20220522 ('NATO').
Zenodo. https://doi.org/10.5281/zenodo.6570228
This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#citation-notice
To silence this citation notice: run 'parallel --citation' once.
Come on: You have run parallel 122 times. Isn't it about time
you run 'parallel --citation' once to silence the citation notice?
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:
Tange, O. (2022, May 22). GNU Parallel 20220522 ('NATO').
Zenodo. https://doi.org/10.5281/zenodo.6570228
This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#citation-notice
To silence this citation notice: run 'parallel --citation' once.
Come on: You have run parallel 123 times. Isn't it about time
you run 'parallel --citation' once to silence the citation notice?
Academic tradition requires you to cite works you base your article on.
If you use programs that use GNU Parallel to process data for an article in a
scientific publication, please cite:
Tange, O. (2022, May 22). GNU Parallel 20220522 ('NATO').
Zenodo. https://doi.org/10.5281/zenodo.6570228
This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
More about funding GNU Parallel and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#citation-notice
To silence this citation notice: run 'parallel --citation' once.
Come on: You have run parallel 124 times. Isn't it about time
you run 'parallel --citation' once to silence the citation notice?
-
ERROR: extract_feature_sequences.pl failed
-
ERROR: PIRATE did not run correctly:
-
ERROR: PIRATE was not able to extract sequences from GFFS
-
ERROR: PIRATE was not able to construct pangenome
-
ERROR: PIRATE was not able to classify paralogs
-
ERROR: PIRATE could not make summary files
-
WARNING: PIRATE could not make binary tree (is fasttree installed)
-
WARNING: PIRATE could not make R plots (are dependencies installed)
-
tests completed
-
temporary files saved to /local_scratch/pbs.5268374.pbs02/Td2byPuwT5
from pirate.
hello hello :) I'm having the same problem.
I think at the moment it's to do with upgrading to BioPerl 1.7+
. use Bio::Perl
doesn't work with BioPerl 1.7+
as far as I can tell. Conda won't allow me to downgrade perl-bioperl
, the newest pirate seems to require it.
extract_feature_sequences.pl
uses use Bio::Perl
. I'm trying to work out what to replace it with at the moment. I'll update if I work it out but I'm not familiar enough with Bioperl yet.
Hope this helps a bit,
Nicola.
from pirate.
By BioPerl 1.7+
I mean perl-bioperl >= 1.7
https://github.com/bioperl/bioperl-live/blob/master/HACKING.md#17-releases
from pirate.
Hi Both,
I have updated extract_feature_sequences to reflect the new bioperl package layout. It works on test data and some of my dummy projects. If you use the most up-to-date master branch (git pull) and let me know if it works for you that would be much appreciated.
All the best,
Sion
from pirate.
Hi Sion,
That worked for me, thank you!
Many thanks,
Nicola.
from pirate.
Dear Sion,
I appreciate your help; however, the problem is still there.
All the best,
Narges
from pirate.
Dear Sion,
The error was finally resolved. Thank you for your support.
Narges
from pirate.
Related Issues (20)
- extract_feature_sequences.pl failed HOT 2
- error observed during "aligning all feature sequences" HOT 2
- Missing genome in output HOT 12
- Output gene sequences to run gene alignment separately HOT 4
- PIRATE_plots.pdf created by plot_summary.R HOT 1
- Error after MCL clustering step HOT 5
- How do you tell which gene families are single-copy or multi-copy? HOT 2
- Feature request: Option to include original IDs and annotations in fasta headers for align_features_sequences script HOT 2
- Average_dose =1 is appropriate to determine whether a gene family is a single copy? HOT 1
- - ERROR: link_clusters.pl failed. HOT 1
- Undefined subroutine &main::translate called HOT 2
- Error when running PIRATE MCL process
- For some single loci, a gene family but for others not. HOT 1
- Bump version in new release HOT 4
- Missing output files and coregenom files HOT 3
- Running on large dataset HOT 2
- stuck at threshold 60 during MCL clustering HOT 3
- PIRATE.pangenome_summary.txt HOT 6
- understanding pirate results
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