Folks
I installed this very useful looking tool repository (fml_gff3togtfhttps://toolshed.g2.bx.psu.edu/view/vipints/fml_gff3togtf) to convert GFF3->BED12 based on this BioStars. https://www.biostars.org/p/85869 It installed fine, but when I run it on ftp://ftp.ncbi.nih.gov/genomes/Viruses/Human_herpesvirus_5_uid14559/NC_006273.gff I get Traceback (most recent call last): File "/share/apps/galaxy/test-shed-tools/toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/6e589f267c14/fml_gff3togtf/gff_to_bed.py", line 18, in <module> import GFFParser File "/share/apps/galaxy/test-shed-tools/toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/6e589f267c14/fml_gff3togtf/GFFParser.py", line 20, in <module> import scipy.io as sio ImportError: No module named scipy.io Anyone know the trick to get the python libraries set up correctly?
(also note that this failed nightly tests on 2015-04-06 - but that looks like a lack of test data/configuration)
I see some other packages (like htseq_counthttps://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count) have numpy as a dependency.... Using the devteam's numpy 1.7 package: https://toolshed.g2.bx.psu.edu/view/devteam/package_numpy_1_7
Regards, Curtis
Research Associate, Informatics Unit Center for Clinical and Translational Science http://bioinformatics.uab.edu University of Alabama at Birmingham
Hi Curtis,
Sorry for the trouble in using the converter package. I will fix the issues which you mentioned below.
For a quick fix, I can point you to my working repository: https://github.com/vipints/GFFtools-GX
This program will help you to convert the gff to 12 column bed file: https://github.com/vipints/GFFtools-GX/blob/master/gff_to_bed.py
the associated galaxy wrapper: https://github.com/vipints/GFFtools-GX/blob/master/gff_to_bed.xml
I know this is not the best way to fix the issue but I will update the public repository soon.
Vipin | Rätsch Lab
On Mon, Apr 6, 2015 at 4:35 PM, Curtis Hendrickson (Campus) <curtish@uab.edu
wrote:
Folks
I installed this very useful looking tool repository (fml_gff3togtf https://toolshed.g2.bx.psu.edu/view/vipints/fml_gff3togtf) to convert GFF3->BED12 based on this BioStars.
https://www.biostars.org/p/85869It installed fine, but when I run it on
ftp://ftp.ncbi.nih.gov/genomes/Viruses/Human_herpesvirus_5_uid14559/NC_006273.gff
I get
Traceback (most recent call last):
File "/share/apps/galaxy/test-shed-tools/ toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/6e589f267c14/fml_gff3togtf/gff_to_bed.py", line 18, in <module>
import GFFParserFile "/share/apps/galaxy/test-shed-tools/ toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/6e589f267c14/fml_gff3togtf/GFFParser.py", line 20, in <module>
import scipy.io as sioImportError: No module named scipy.io
Anyone know the trick to get the python libraries set up correctly?
(also note that this failed nightly tests on 2015-04-06 – but that looks like a lack of test data/configuration)
I see some other packages (like htseq_count https://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count) have numpy as a dependency…. Using the devteam’s numpy 1.7 package:
https://toolshed.g2.bx.psu.edu/view/devteam/package_numpy_1_7
Regards,
Curtis
Research Associate, Informatics Unit
Center for Clinical and Translational Science
University of Alabama at Birmingham
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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If you are installing scipy from source (and I think that is how galaxy and pip both do it), then you need a fortran compiler installed.
-Will
On Mon, Apr 6, 2015 at 1:35 PM, Curtis Hendrickson (Campus) <curtish@uab.edu
wrote:
Folks
I installed this very useful looking tool repository (fml_gff3togtf https://toolshed.g2.bx.psu.edu/view/vipints/fml_gff3togtf) to convert GFF3->BED12 based on this BioStars.
https://www.biostars.org/p/85869It installed fine, but when I run it on
ftp://ftp.ncbi.nih.gov/genomes/Viruses/Human_herpesvirus_5_uid14559/NC_006273.gff
I get
Traceback (most recent call last):
File "/share/apps/galaxy/test-shed-tools/ toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/6e589f267c14/fml_gff3togtf/gff_to_bed.py", line 18, in <module>
import GFFParserFile "/share/apps/galaxy/test-shed-tools/ toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/6e589f267c14/fml_gff3togtf/GFFParser.py", line 20, in <module>
import scipy.io as sioImportError: No module named scipy.io
Anyone know the trick to get the python libraries set up correctly?
(also note that this failed nightly tests on 2015-04-06 – but that looks like a lack of test data/configuration)
I see some other packages (like htseq_count https://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count) have numpy as a dependency…. Using the devteam’s numpy 1.7 package:
https://toolshed.g2.bx.psu.edu/view/devteam/package_numpy_1_7
Regards,
Curtis
Research Associate, Informatics Unit
Center for Clinical and Translational Science
University of Alabama at Birmingham
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
galaxy-dev@lists.galaxyproject.org
-
Curtis Hendrickson (Campus) -
Vipin TS -
Will Holtz