fml_gff3togtf: GTF-to-BED failes on numpy in Galaxy

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fml_gff3togtf: GTF-to-BED failes on numpy in Galaxy

Curtis Hendrickeduson

Folks

 

I installed this very useful looking tool repository (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_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

 


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Re: fml_gff3togtf: GTF-to-BED failes on numpy in Galaxy

Vipin TS
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: 

This program will help you to convert the gff to 12 column bed file:

the associated galaxy wrapper:

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) <[hidden email]> wrote:

Folks

 

I installed this very useful looking tool repository (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_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

 


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in your mail client.  To manage your subscriptions to this
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: fml_gff3togtf: GTF-to-BED failes on numpy in Galaxy

Will Holtz
In reply to this post by Curtis Hendrickeduson
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) <[hidden email]> wrote:

Folks

 

I installed this very useful looking tool repository (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_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

 


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___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
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