importing a large number of samples via a sample sheet
Bumping this question....no response in over a week... Hi all - I've recently come back to Galaxy to see how its progressed over the last few years. The tools shed is completely new to me and will take some exploring on my part. My immediate question is if there is a way to import a large number of samples associated with a project via a sample sheet (txt) file? I have a text file with 3 columns: sample name, location of fastq files. I haven't seen a way to import this and haven't seen anything in the docs either. I suspect the answer is no, but I'm hoping the answer is actually yes....?
Hey Ryan, Sorry this fell through the cracks. A script to import large sets of files to data libraries, for example, would be really easy to implement using the Galaxy API. There are several examples in the /scripts/api folder of your distribution ( https://bitbucket.org/galaxy/galaxy-central/src/7f247bf156dfc7cfa7f764cf9757...). I can find an explicit example of this if you're interested. -Dannon On Thu, Nov 13, 2014 at 9:08 AM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Bumping this question....no response in over a week...
Hi all - I've recently come back to Galaxy to see how its progressed over the last few years. The tools shed is completely new to me and will take some exploring on my part.
My immediate question is if there is a way to import a large number of samples associated with a project via a sample sheet (txt) file? I have a text file with 3 columns: sample name, location of fastq files.
I haven't seen a way to import this and haven't seen anything in the docs either. I suspect the answer is no, but I'm hoping the answer is actually yes....?
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Let me see if I can find what I need and if I need any help, I'll let you know. Thanks! On Thu, Nov 13, 2014 at 12:14 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hey Ryan,
Sorry this fell through the cracks. A script to import large sets of files to data libraries, for example, would be really easy to implement using the Galaxy API. There are several examples in the /scripts/api folder of your distribution ( https://bitbucket.org/galaxy/galaxy-central/src/7f247bf156dfc7cfa7f764cf9757...). I can find an explicit example of this if you're interested.
-Dannon
On Thu, Nov 13, 2014 at 9:08 AM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Bumping this question....no response in over a week...
Hi all - I've recently come back to Galaxy to see how its progressed over the last few years. The tools shed is completely new to me and will take some exploring on my part.
My immediate question is if there is a way to import a large number of samples associated with a project via a sample sheet (txt) file? I have a text file with 3 columns: sample name, location of fastq files.
I haven't seen a way to import this and haven't seen anything in the docs either. I suspect the answer is no, but I'm hoping the answer is actually yes....?
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
I guess I am going to need a little help to get started... I'm trying to use display.py. I've followed the directions and created an api key. When I run: ./display.py my_key http://myhost:myport/api/libraries I get the a 403 forbidden. however, when I enter the URL in a brower: http://myhost:myport/api/libraries?key=my_key I get a JSON response with the libraries I've already added. Something must be wrong at the script level? On Thu, Nov 13, 2014 at 12:50 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Let me see if I can find what I need and if I need any help, I'll let you know. Thanks!
On Thu, Nov 13, 2014 at 12:14 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hey Ryan,
Sorry this fell through the cracks. A script to import large sets of files to data libraries, for example, would be really easy to implement using the Galaxy API. There are several examples in the /scripts/api folder of your distribution ( https://bitbucket.org/galaxy/galaxy-central/src/7f247bf156dfc7cfa7f764cf9757...). I can find an explicit example of this if you're interested.
-Dannon
On Thu, Nov 13, 2014 at 9:08 AM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Bumping this question....no response in over a week...
Hi all - I've recently come back to Galaxy to see how its progressed over the last few years. The tools shed is completely new to me and will take some exploring on my part.
My immediate question is if there is a way to import a large number of samples associated with a project via a sample sheet (txt) file? I have a text file with 3 columns: sample name, location of fastq files.
I haven't seen a way to import this and haven't seen anything in the docs either. I suspect the answer is no, but I'm hoping the answer is actually yes....?
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hey Ryan, Sorry this took a long while for me to get back to, again. I probably should have pointed you here to start with, but bioblend (a nice python layer on top of the raw galaxy API) has a much friendlier interface and is what you'd probably want to use for this kind of script. Here's an example specifically of uploading from filepaths to a data library: http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/docs.html#upload-f... -Dannon On Thu, Nov 13, 2014 at 1:51 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
I guess I am going to need a little help to get started...
I'm trying to use display.py. I've followed the directions and created an api key. When I run:
./display.py my_key http://myhost:myport/api/libraries
I get the a 403 forbidden. however, when I enter the URL in a brower:
http://myhost:myport/api/libraries?key=my_key
I get a JSON response with the libraries I've already added. Something must be wrong at the script level?
On Thu, Nov 13, 2014 at 12:50 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Let me see if I can find what I need and if I need any help, I'll let you know. Thanks!
On Thu, Nov 13, 2014 at 12:14 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hey Ryan,
Sorry this fell through the cracks. A script to import large sets of files to data libraries, for example, would be really easy to implement using the Galaxy API. There are several examples in the /scripts/api folder of your distribution ( https://bitbucket.org/galaxy/galaxy-central/src/7f247bf156dfc7cfa7f764cf9757...). I can find an explicit example of this if you're interested.
-Dannon
On Thu, Nov 13, 2014 at 9:08 AM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Bumping this question....no response in over a week...
Hi all - I've recently come back to Galaxy to see how its progressed over the last few years. The tools shed is completely new to me and will take some exploring on my part.
My immediate question is if there is a way to import a large number of samples associated with a project via a sample sheet (txt) file? I have a text file with 3 columns: sample name, location of fastq files.
I haven't seen a way to import this and haven't seen anything in the docs either. I suspect the answer is no, but I'm hoping the answer is actually yes....?
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
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Dannon Baker -
Ryan G