Comments (3)
andrewjpage
commented on June 3, 2024
Yes, it's actually only been tested with prokka gff3 files, and has been
used for 11,000 submissions. It requires genome tools, which will only work
on Linux(which is probably a show stopper).
Andrew
On 14 Mar 2015 04:23, "Torsten Seemann" [email protected] wrote:
Does the GFF3 file that Prokka produces satisfy the input requirements for
this script?I would really like to ditch tbl2asn !
—
Reply to this email directly or view it on GitHub
#23.
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satta
commented on June 3, 2024
Actually the GenomeTools Python bindings (which indeed had problems on other platforms) have recently been fixed (genometools/genometools#211) to the point where at least the Python testsuite passes now on Mac OS X as well. I didn't try it with gff3toembl yet, but if you try just let me know if anything fails.
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tseemann
commented on June 3, 2024
I've just moved jobs, and setting up from scratch. Decided to use LinuxBrew for package management, as the team have already done lots of homebrew-science formulae, which I am slowly adding to.
(genometools is in Brew, but if fails on LinuxBrew.)
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Related Issues (20)
- v1.0.0 vs v1.0 HOT 3
- Failure to install on Biolinux HOT 29
- Python 3 support HOT 1
- Non-standard indentation of Python code HOT 1
- Document versions of Python supported HOT 5
- self.assertItemsEqual is Python 2.7 only HOT 2
- Format for listing authors not defined HOT 1
- Long author lists break instead of line wrapping HOT 3
- Should unescape %2C in GFF column 9 as comma in EMBL HOT 2
- Bad line-breaks in long words, consider breaking at hyphenation HOT 4
- Can we pip install this? HOT 2
- I have added this to my brew repo (updated to 1.0.9) HOT 2
- linuxbrew recipe needs updating HOT 1
- mac brew install does not work. HOT 1
- Change PROKKA to Prokka in repo description HOT 1
- Sequence header SQ line can exceed 80 characters HOT 5
- How to prepare a novel strain/isolate of a bacteria? HOT 11
- Installation and running problems HOT 3
- No module named 'gt' from bioconda install
- Cannot open *.gff_fixed.gff: No such file or directory
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