Only custom genomes for uploads in data libraries
Hi, I'm running latest galaxy-dist locally. When I try to upload a dataset to a data library through Admin, I only get the two custom genomes I have created for visualizations. If I use the regular upload tool under "Get data", I do get to choose any of the genomes in: tool-data/shared/ucsc/builds.txt I tried deleting the custom genomes and then the dropbox menu in the data libraries upload form is empty. Is there something I'm missing? I would like to be able to select any genome available, custom or not. Thanks, Carlos
So my quick hack broke this: https://bitbucket.org/galaxy/galaxy-central/commits/0ec7f0b6dec8707b6f4d1144... To fix this and related issues, I finally took the step of unifying all builds and build information into a single Python data structure: https://bitbucket.org/galaxy/galaxy-central/commits/f36d5d615dd4/ To fix this, then, you can wait for the next Galaxy dist or apply the above changeset manually. Best, J. On Jan 25, 2013, at 12:02 PM, Carlos Borroto wrote:
Hi,
I'm running latest galaxy-dist locally. When I try to upload a dataset to a data library through Admin, I only get the two custom genomes I have created for visualizations. If I use the regular upload tool under "Get data", I do get to choose any of the genomes in: tool-data/shared/ucsc/builds.txt
I tried deleting the custom genomes and then the dropbox menu in the data libraries upload form is empty.
Is there something I'm missing? I would like to be able to select any genome available, custom or not.
Thanks, Carlos
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So my quick hack broke this:
https://bitbucket.org/galaxy/galaxy-central/commits/0ec7f0b6dec8707b6f4d1144...
To fix this and related issues, I finally took the step of unifying all builds and build information into a single Python data structure:
https://bitbucket.org/galaxy/galaxy-central/commits/f36d5d615dd4/
To fix this, then, you can wait for the next Galaxy dist or apply the above changeset manually.
Actually, there an easier way to fix this without patching your Galaxy installation. Builds will show up in the library dbkey box if there's a chromosome length file associated with the build. Chromosome length files are used in some format converters (e.g. wig/bedgraph-to-bigwig) and for visualization. You can download len files by doing the following: (1) Uncomment/add len_file_path to your universe.wsgi.ini file, e.g.: len_file_path = tool-data/shared/ucsc/chrom (2) Run these commands from your Galaxy install to download len files from UCSC: mkdir ./tool-data/shared/ucsc/chrom/ python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/ (3) Restart Galaxy. Best, J.
On Sun, Jan 27, 2013 at 10:04 AM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Actually, there an easier way to fix this without patching your Galaxy installation. Builds will show up in the library dbkey box if there's a chromosome length file associated with the build. Chromosome length files are used in some format converters (e.g. wig/bedgraph-to-bigwig) and for visualization.
You can download len files by doing the following:
(1) Uncomment/add len_file_path to your universe.wsgi.ini file, e.g.:
len_file_path = tool-data/shared/ucsc/chrom
(2) Run these commands from your Galaxy install to download len files from UCSC:
mkdir ./tool-data/shared/ucsc/chrom/ python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/
(3) Restart Galaxy.
Thanks Jeremy, I will try this and report back.
On Mon, Jan 28, 2013 at 10:40 AM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
On Sun, Jan 27, 2013 at 10:04 AM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Actually, there an easier way to fix this without patching your Galaxy installation. Builds will show up in the library dbkey box if there's a chromosome length file associated with the build. Chromosome length files are used in some format converters (e.g. wig/bedgraph-to-bigwig) and for visualization.
You can download len files by doing the following:
(1) Uncomment/add len_file_path to your universe.wsgi.ini file, e.g.:
len_file_path = tool-data/shared/ucsc/chrom
(2) Run these commands from your Galaxy install to download len files from UCSC:
mkdir ./tool-data/shared/ucsc/chrom/ python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/
(3) Restart Galaxy.
Thanks Jeremy, I will try this and report back.
I can confirm following these steps fix this issue. Thanks a lot, Carlos
participants (2)
-
Carlos Borroto -
Jeremy Goecks