[galaxy-dev] create a folder inside a library folder using API
Hi,
How can I create a folder inside another library folder?
I tried:
lib_create_data = {
'name':'mm9',
'create_type': 'folder',
}
submit(api_key, api_url + "libraries/%s/contents" % library_id,
lib_create_data, return_formatted=False)
Where library_id is the upper library folder id.
But this failed with the following error:
Error. "Missing requred 'folder_id' parameter."
Does someone know how to do this?
Thanks,
Hagai
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[galaxy-dev] tasks (parralelism) and from_work_dir bug
Hi, I have tried to use tasks with tophat2, but I got the following bug. > multi.py +153 msg = 'nothing to merge for %s (expected %i files)' \ % (output_file_name, len(task_dirs)) This occurs because tophat2 tool uses from_work_dir feature to get the output files. But on the line: output_files = [ f for f in output_files if os.path.exists(f) ] It returnes an empty list because no real output files exists. Did anyone else have tried this before? Hagai ___ 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/
Re: [galaxy-dev] gene annotation file (gtf)
That's a great idea. I have used data libraries from the api. Can I set a data library file as the input for a tool using the browser? Hagai On Thu, Apr 4, 2013 at 5:31 PM, Hans-Rudolf Hotz wrote: > > > On 04/04/2013 04:10 PM, Hagai Cohen wrote: > >> Hi, >> Is is possible to configure gene annotation file files inside galaxy per >> genome internally? >> As in bowtie indices or something similiar. >> I don't want to upload the ucsc constant gtf files on each history I >> need them. >> >> > Have you considered creating a data library? (http://wiki.galaxyproject.** > org/Admin/DataLibraries/**Libraries<http://wiki.galaxyproject.org/Admin/DataLibraries/Libraries> > ) > > you can the re-use the data without downloading again and without > duplicating. > > Regards, Hans-Rudolf > > > > Thanks for the help, >> Hagai >> >> >> >> __**_ >> 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/<http://galaxyproject.org/search/mailinglists/> >> >> ___ 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/
[galaxy-dev] gene annotation file (gtf)
Hi, Is is possible to configure gene annotation file files inside galaxy per genome internally? As in bowtie indices or something similiar. I don't want to upload the ucsc constant gtf files on each history I need them. Thanks for the help, Hagai ___ 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/
Re: [galaxy-dev] show urls in csv (in eye mode)
Hi,
I found that in order to change static/scripts/mvc/data.js, I had to delete
static/scripts/packed/mvc/data.js.
After doing so, I have added the following patch in order to add links
inside tabular view.
else if (column_types[index] === 'str' || column_types === 'list') {
/* Left align all str columns, right align the rest */
-return $('').addClass('stringalign').text(cell_contents);
+ var temp =
$('').addClass('stringalign').text(cell_contents);
+ var text = Linkify(temp.text());
+ return temp.html(text);
}
I think this is better from the security aspect.
Now it looks like this:
chr147474796734088968.2326.21
http://genome.ucsc.edu/cgi-bin/hgTracks?db=m9&position=chr1:4747-4119<http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr1:4770447-4781119>
chr149984769194991695.9322.77
http://genome.ucsc.edu/cgi-bin/hgTracks?db=m9&position=chr1:4798-4316<http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr1:4792498-4803416>
I hope this might be useful for others as well.
Hagai
On Mon, Mar 18, 2013 at 6:14 PM, Hagai Cohen wrote:
> Hi,
> I want to do this using a function which converts each URL into an html
> link ( after the .text() was called).
> (For example to use: https://github.com/maranomynet/linkify).
> But now the galaxy code is a bit different and I can't find where should I
> change the code.
>
> I have found the _renderCell function here: static/scripts/mvc/data.js,
> but I didn't succeed in changing it to add links to the html.
> What am I doing wrong?
>
> Thanks,
> Hagai
>
>
>
> On Sun, Feb 3, 2013 at 1:06 PM, Hagai Cohen wrote:
>
>> Right.
>> I will convert it to text, allowing only simple links ( with href
>> only) to be shown.
>> Thanks,
>> Hagai
>>
>>
>>
>> On Wed, Jan 30, 2013 at 8:03 PM, James Taylor wrote:
>>
>>> You may want to be careful with this solution because it allows script
>>> injection, any HTML including javascript in the uploaded tabular file
>>> will be executed by the .html call, with complete access to everything
>>> in the Galaxy browser window (like your session cookies).
>>>
>>> --
>>> James Taylor, Assistant Professor, Biology/CS, Emory University
>>>
>>>
>>> On Tue, Jan 29, 2013 at 7:18 AM, Hagai Cohen wrote:
>>> > Hi,
>>> > I found a simple solution.
>>> >
>>> > In the file:
>>> > templates/dataset/tabular_chunked.mako
>>> > inside the method: renderCell - replace all jQuery .text(..) calls with
>>> > .html(..) calls.
>>> >
>>> > Note:
>>> > Any entry in the csv with html syntax will be shown like html (links,
>>> tags.
>>> > etc).
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> > On Tue, Jan 29, 2013 at 1:39 PM, Hagai Cohen
>>> wrote:
>>> >>
>>> >> Hi,
>>> >> I have a tool which outputs a csv file with links.
>>> >> When I press the eye icon - I would like these links to be shown as
>>> links
>>> >> in the browser.
>>> >> It is possible?
>>> >>
>>> >> Thanks,
>>> >> Hagai
>>> >
>>> >
>>> >
>>> > ___
>>> > 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/
>>>
>>
>>
>
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[galaxy-dev] Different display ratio (Tools, Center & History)
Hi, How is it possible to change the deafult display ratio in galaxy? (The ratio between the tools, center & history) Thanks, Hagai ___ 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/
Re: [galaxy-dev] show urls in csv (in eye mode)
Hi, I want to do this using a function which converts each URL into an html link ( after the .text() was called). (For example to use: https://github.com/maranomynet/linkify). But now the galaxy code is a bit different and I can't find where should I change the code. I have found the _renderCell function here: static/scripts/mvc/data.js, but I didn't succeed in changing it to add links to the html. What am I doing wrong? Thanks, Hagai On Sun, Feb 3, 2013 at 1:06 PM, Hagai Cohen wrote: > Right. > I will convert it to text, allowing only simple links ( with href only) > to be shown. > Thanks, > Hagai > > > > On Wed, Jan 30, 2013 at 8:03 PM, James Taylor wrote: > >> You may want to be careful with this solution because it allows script >> injection, any HTML including javascript in the uploaded tabular file >> will be executed by the .html call, with complete access to everything >> in the Galaxy browser window (like your session cookies). >> >> -- >> James Taylor, Assistant Professor, Biology/CS, Emory University >> >> >> On Tue, Jan 29, 2013 at 7:18 AM, Hagai Cohen wrote: >> > Hi, >> > I found a simple solution. >> > >> > In the file: >> > templates/dataset/tabular_chunked.mako >> > inside the method: renderCell - replace all jQuery .text(..) calls with >> > .html(..) calls. >> > >> > Note: >> > Any entry in the csv with html syntax will be shown like html (links, >> tags. >> > etc). >> > >> > >> > >> > >> > >> > >> > On Tue, Jan 29, 2013 at 1:39 PM, Hagai Cohen wrote: >> >> >> >> Hi, >> >> I have a tool which outputs a csv file with links. >> >> When I press the eye icon - I would like these links to be shown as >> links >> >> in the browser. >> >> It is possible? >> >> >> >> Thanks, >> >> Hagai >> > >> > >> > >> > ___ >> > 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/ >> > > ___ 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/
Re: [galaxy-dev] bowtie-wrapper
You can change the bowtie wrapper to save the stderr of the bowtie part. The command line is (bowtie2_wrapper.py): cmd = 'bowtie2 %s -x %s %s %s | samtools view -Su - | samtools sort -o - - > %s' Change it to something like: cmd = 'bowtie2 %s -x %s %s %s 2> bowtie_stderr_filename | samtools view -Su - | samtools sort -o - - > %s' Where bowtie_stderr_filename is a temporary filename. And concat this before the stderr afterwards (of the whole command). Hopefully, the official bowtie-wrapper will have this addition too. Hagai On Mon, Feb 25, 2013 at 1:29 PM, Alexander Kurze < alexander.ku...@bioch.ox.ac.uk> wrote: > Hello, > > I am using the bowtie-wrapper on my locally installed galaxy server to > align reads. However I missing the stats read-out. Is there any possibility > to include statistics about unaligned reads? > > If I use bowtie vi comman line I get following output: > > > bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam > End-to-end 2/3-mismatch full-index search: 01:00:21 > # reads processed: 12084153 > # reads with at least one reported alignment: 9391748 (77.72%) > # reads that failed to align: 2692405 (22.28%) > Reported 30293838 alignments to 1 output stream(s) > > > The output should be normally saved in the stderr but unfortunatly the > stderr is somehow deleted after the alignment job is done in bowtie under > galaxy. > > Any idea how I can still access the stats? > > Thanks, > > Alex > > -- > Alexander Kurze, DPhil > University of Oxford > Department of Biochemistry > South Parks Road > Oxford, OX1 3QU > United Kingdom > > Tel: +44 1865 613 230 > Fax:+44 1865 613 341 > > ___ > 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/ > ___ 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/
Re: [galaxy-dev] Preffered way of running a tool on multiple input files
Hi John, I'm using your bitbucket fork.I still didn't finish all the needed job but meanwhile it works great. The two tools you add: multi-upload & split - works great too - and are all what I needed. (I had only one patch which I had to add somewhere - I'm still trying to understand the galaxy code there.) The difference between tool which accepts input file and a tool which accepts multi-input-file is nice. Currently, I'm gone use this. I hope the official release will have similar feature in the future. Thanks, Hagai On Wed, Feb 13, 2013 at 9:56 AM, Hagai Cohen wrote: > > John, that's seems great. > I will read this stuff and see if I can use it (The bed format isn't that > essential, bowtie can bam instead). > > If it wont work I will try the other solution which doesn't need to change > the galaxy own code (Creating hundreds of workflow run, linking to their > outputs and running last workflow with the merging tool - this solution > also distribute in a better way). > > Because galaxy is used a lot on sequencers output, I think someday it > should support this kind of jobs internally. > When I will have a running solution, I will publish what solution I have > used. > > Its really great to know I'm not the first one to attack this problem. > Thanks for the advices. > Hagai > > > > > > On Tue, Feb 12, 2013 at 5:42 PM, Joachim Jacob |VIB| > wrote: > >> You cannot directly couple different workflows. >> >> But you could indeed copy all outputs of the different workflows into one >> history, and create a separate workflow with your tool to work on all those >> input files. >> >> Cheers, >> >> Joachim >> >> Joachim Jacob >> >> Rijvisschestraat 120, 9052 Zwijnaarde >> Tel: +32 9 244.66.34 >> Bioinformatics Training and Services (BITS) >> http://www.bits.vib.be >> @bitsatvib >> >> On 02/12/2013 04:31 PM, Hagai Cohen wrote: >> >>> >>> Thanks for your answer. >>> I figured that there is an option to run a workflow on multiple files, >>> but I can't merge the outputs afterwardsl. I would like the workflow to >>> return one final output. >>> >>> But you gave me another idea. >>> Can I somehow tell one workflow to run on other workflow output? >>> If this can be done, I can run 100 different workflows with bowtie & >>> statistics, each working on one fastq file, than run another workflow which >>> gets 100 xls inputs and merge them to one. >>> >>> >>> >>> >>> On Tue, Feb 12, 2013 at 5:20 PM, Joachim Jacob |VIB| < >>> joachim.ja...@vib.be <mailto:joachim.ja...@vib.be>> wrote: >>> >>> Hi Hagai, >>> >>> Actually, using a workflow, you are able to select multiple input >>> files, and let the workflow run separately on all input files. >>> >>> I would proceed by creating a data library for all your fastq >>> files, which you can upload via FTP, or via a system directory. >>> You can use a sample of your fastq files to create the steps in a >>> history you want to perform, and extract a workflow out of it. >>> Next, copy all fastq files from a data library in a new history, >>> and run your workflow on the all input files. >>> >>> I hope this helps you further, >>> Joachim >>> >>> >>> Joachim Jacob >>> >>> Rijvisschestraat 120, 9052 Zwijnaarde >>> Tel: +32 9 244.66.34 >>> >>> Bioinformatics Training and Services (BITS) >>> http://www.bits.vib.be >>> @bitsatvib >>> >>> >>> On 02/12/2013 04:02 PM, Hagai Cohen wrote: >>> >>> Hi, >>> I'm looking for a preferred way of running Bowtie (or any >>> other tool) on multiple input files and run statistics on the >>> Bowtie output afterwards. >>> >>> The input is a directory of files fastq1..fastq100 >>> The bowtie output should be bed1...bed100 >>> The statistics tool should run on bed1...bed100 and return >>> xls1..xls100 >>> Then I will write a tool which will get xls1..xls100 and merge >>> them to one final output. >>> >>> I searched for a smiliar cases, and I couldn't figure anyone >>> which had this problem before. >>> Can't use the parallelism tag, because what will be the input
Re: [galaxy-dev] Preffered way of running a tool on multiple input files
John, that's seems great. I will read this stuff and see if I can use it (The bed format isn't that essential, bowtie can bam instead). If it wont work I will try the other solution which doesn't need to change the galaxy own code (Creating hundreds of workflow run, linking to their outputs and running last workflow with the merging tool - this solution also distribute in a better way). Because galaxy is used a lot on sequencers output, I think someday it should support this kind of jobs internally. When I will have a running solution, I will publish what solution I have used. Its really great to know I'm not the first one to attack this problem. Thanks for the advices. Hagai On Tue, Feb 12, 2013 at 5:42 PM, Joachim Jacob |VIB| wrote: > You cannot directly couple different workflows. > > But you could indeed copy all outputs of the different workflows into one > history, and create a separate workflow with your tool to work on all those > input files. > > Cheers, > > Joachim > > Joachim Jacob > > Rijvisschestraat 120, 9052 Zwijnaarde > Tel: +32 9 244.66.34 > Bioinformatics Training and Services (BITS) > http://www.bits.vib.be > @bitsatvib > > On 02/12/2013 04:31 PM, Hagai Cohen wrote: > >> >> Thanks for your answer. >> I figured that there is an option to run a workflow on multiple files, >> but I can't merge the outputs afterwardsl. I would like the workflow to >> return one final output. >> >> But you gave me another idea. >> Can I somehow tell one workflow to run on other workflow output? >> If this can be done, I can run 100 different workflows with bowtie & >> statistics, each working on one fastq file, than run another workflow which >> gets 100 xls inputs and merge them to one. >> >> >> >> >> On Tue, Feb 12, 2013 at 5:20 PM, Joachim Jacob |VIB| < >> joachim.ja...@vib.be <mailto:joachim.ja...@vib.be>> wrote: >> >> Hi Hagai, >> >> Actually, using a workflow, you are able to select multiple input >> files, and let the workflow run separately on all input files. >> >> I would proceed by creating a data library for all your fastq >> files, which you can upload via FTP, or via a system directory. >> You can use a sample of your fastq files to create the steps in a >> history you want to perform, and extract a workflow out of it. >> Next, copy all fastq files from a data library in a new history, >> and run your workflow on the all input files. >> >> I hope this helps you further, >> Joachim >> >> >> Joachim Jacob >> >> Rijvisschestraat 120, 9052 Zwijnaarde >> Tel: +32 9 244.66.34 >> >> Bioinformatics Training and Services (BITS) >> http://www.bits.vib.be >> @bitsatvib >> >> >> On 02/12/2013 04:02 PM, Hagai Cohen wrote: >> >> Hi, >> I'm looking for a preferred way of running Bowtie (or any >> other tool) on multiple input files and run statistics on the >> Bowtie output afterwards. >> >> The input is a directory of files fastq1..fastq100 >> The bowtie output should be bed1...bed100 >> The statistics tool should run on bed1...bed100 and return >> xls1..xls100 >> Then I will write a tool which will get xls1..xls100 and merge >> them to one final output. >> >> I searched for a smiliar cases, and I couldn't figure anyone >> which had this problem before. >> Can't use the parallelism tag, because what will be the input >> for each tool? it should be a fastq file not a directory of >> fastq files. >> Neither I would like to run each fastq file in a different >> workflow - creating a mess. >> >> I thought only on two solutions: >> 1. Implement new datatypes: bed_dir & fastq_dir and implements >> new tool wrappers which will get a folder instead of a file. >> 2. merge the input files before sending to bowtie, and use >> parallelism tag to make them be splitted & merged again on >> each tool. >> >> Does anyone has any better suggestion? >> >> Thanks, >> Hagai >> >> >> >> >> >> >> >> >> >> >> >> __**_ >> 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/ >> >> >> >> > ___ 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/
Re: [galaxy-dev] Preffered way of running a tool on multiple input files
Thanks for your answer. I figured that there is an option to run a workflow on multiple files, but I can't merge the outputs afterwardsl. I would like the workflow to return one final output. But you gave me another idea. Can I somehow tell one workflow to run on other workflow output? If this can be done, I can run 100 different workflows with bowtie & statistics, each working on one fastq file, than run another workflow which gets 100 xls inputs and merge them to one. On Tue, Feb 12, 2013 at 5:20 PM, Joachim Jacob |VIB| wrote: > Hi Hagai, > > Actually, using a workflow, you are able to select multiple input files, > and let the workflow run separately on all input files. > > I would proceed by creating a data library for all your fastq files, which > you can upload via FTP, or via a system directory. > You can use a sample of your fastq files to create the steps in a history > you want to perform, and extract a workflow out of it. > Next, copy all fastq files from a data library in a new history, and run > your workflow on the all input files. > > I hope this helps you further, > Joachim > > > Joachim Jacob > > Rijvisschestraat 120, 9052 Zwijnaarde > Tel: +32 9 244.66.34 > Bioinformatics Training and Services (BITS) > http://www.bits.vib.be > @bitsatvib > > > On 02/12/2013 04:02 PM, Hagai Cohen wrote: > >> Hi, >> I'm looking for a preferred way of running Bowtie (or any other tool) on >> multiple input files and run statistics on the Bowtie output afterwards. >> >> The input is a directory of files fastq1..fastq100 >> The bowtie output should be bed1...bed100 >> The statistics tool should run on bed1...bed100 and return xls1..xls100 >> Then I will write a tool which will get xls1..xls100 and merge them to >> one final output. >> >> I searched for a smiliar cases, and I couldn't figure anyone which had >> this problem before. >> Can't use the parallelism tag, because what will be the input for each >> tool? it should be a fastq file not a directory of fastq files. >> Neither I would like to run each fastq file in a different workflow - >> creating a mess. >> >> I thought only on two solutions: >> 1. Implement new datatypes: bed_dir & fastq_dir and implements new tool >> wrappers which will get a folder instead of a file. >> 2. merge the input files before sending to bowtie, and use parallelism >> tag to make them be splitted & merged again on each tool. >> >> Does anyone has any better suggestion? >> >> Thanks, >> Hagai >> >> >> >> >> >> >> >> >> >> >> >> __**_ >> 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/ >> > > ___ 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/
[galaxy-dev] Preffered way of running a tool on multiple input files
Hi, I'm looking for a preferred way of running Bowtie (or any other tool) on multiple input files and run statistics on the Bowtie output afterwards. The input is a directory of files fastq1..fastq100 The bowtie output should be bed1...bed100 The statistics tool should run on bed1...bed100 and return xls1..xls100 Then I will write a tool which will get xls1..xls100 and merge them to one final output. I searched for a smiliar cases, and I couldn't figure anyone which had this problem before. Can't use the parallelism tag, because what will be the input for each tool? it should be a fastq file not a directory of fastq files. Neither I would like to run each fastq file in a different workflow - creating a mess. I thought only on two solutions: 1. Implement new datatypes: bed_dir & fastq_dir and implements new tool wrappers which will get a folder instead of a file. 2. merge the input files before sending to bowtie, and use parallelism tag to make them be splitted & merged again on each tool. Does anyone has any better suggestion? Thanks, Hagai ___ 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/
[galaxy-dev] galaxy assumed linux shell
Hi, There are couple of Linux shells: bash, sh, zsh, csh. etc I would like to know if Galaxy is written to be supported on a specific one or it is written to support any linux shell? I'm asking this, because I want to add some features and I want to know what shell should I support? Or should write cross-shell code? In Dramaa runner, for example, it uses sh shell (inside drm_template inside drmaa.py), so any job that is run through this runner should support sh. Thanks, Hagai ___ 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/
Re: [galaxy-dev] show urls in csv (in eye mode)
Right. I will convert it to text, allowing only simple links ( with href only) to be shown. Thanks, Hagai On Wed, Jan 30, 2013 at 8:03 PM, James Taylor wrote: > You may want to be careful with this solution because it allows script > injection, any HTML including javascript in the uploaded tabular file > will be executed by the .html call, with complete access to everything > in the Galaxy browser window (like your session cookies). > > -- > James Taylor, Assistant Professor, Biology/CS, Emory University > > > On Tue, Jan 29, 2013 at 7:18 AM, Hagai Cohen wrote: > > Hi, > > I found a simple solution. > > > > In the file: > > templates/dataset/tabular_chunked.mako > > inside the method: renderCell - replace all jQuery .text(..) calls with > > .html(..) calls. > > > > Note: > > Any entry in the csv with html syntax will be shown like html (links, > tags. > > etc). > > > > > > > > > > > > > > On Tue, Jan 29, 2013 at 1:39 PM, Hagai Cohen wrote: > >> > >> Hi, > >> I have a tool which outputs a csv file with links. > >> When I press the eye icon - I would like these links to be shown as > links > >> in the browser. > >> It is possible? > >> > >> Thanks, > >> Hagai > > > > > > > > ___ > > 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/ > ___ 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/
Re: [galaxy-dev] show urls in csv (in eye mode)
Hi, I found a simple solution. In the file: templates/dataset/tabular_chunked.mako inside the method: renderCell - replace all jQuery .text(..) calls with .html(..) calls. Note: Any entry in the csv with html syntax will be shown like html (links, tags. etc). On Tue, Jan 29, 2013 at 1:39 PM, Hagai Cohen wrote: > Hi, > I have a tool which outputs a csv file with links. > When I press the eye icon - I would like these links to be shown as links > in the browser. > It is possible? > > Thanks, > Hagai > ___ 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/
[galaxy-dev] show urls in csv (in eye mode)
Hi, I have a tool which outputs a csv file with links. When I press the eye icon - I would like these links to be shown as links in the browser. It is possible? Thanks, Hagai ___ 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/
[galaxy-dev] rerun tool in a workflow
Hi, is it possible that when I rerun a tool it will also rerun the tools that depends on it? ___ 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/
[galaxy-dev] different path for galaxy in cluster
Hi, I have a problem with my galaxy local installation working with a cluster. On the server my galaxy dir path is X, but on the cluster it is Y (same directory but different soft links). Is it possible to config the path of the galaxy installation (GALAXY_DIR) which will be send to the nodes? Thanks, Hagai ___ 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/
Re: [galaxy-dev] user creation using API
This is really helpful, Works great. Thanks, Hagai On Mon, Jan 7, 2013 at 5:13 PM, John Chilton wrote: > I am pretty confident there is no way to do this via the API > currently, though I imagine it wouldn't be terribly complicated to add > and the community would appreciate the contribution. If API-based > access isn't a strong requirement and you have direct access to the > Galaxy server here is a script-template I have used to automatically > create users: > > https://gist.github.com/4475646 > > The above gist is probably enough to get going, but here is the full > context of how I create such a file if that is of interest: > > https://github.com/jmchilton/cloudbiolinux/blob/deploy/cloudbio/deploy/galaxy.py > > -John > > On Mon, Jan 7, 2013 at 3:37 AM, Hagai Cohen wrote: > > Hi, > > I would like to auto create users on my local Galaxy instance. > > > > I saw that in the "create user" on the API, I should enable > use_remote_user > > (which as I understand means that I have to use Apache or nginx). > > Is there another way besides using Apache to create users automatically? > > > > Thanks, > > Hagai > > > > > > ___ > > 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/ > ___ 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/
[galaxy-dev] user creation using API
Hi, I would like to auto create users on my local Galaxy instance. I saw that in the "create user" on the API, I should enable use_remote_user (which as I understand means that I have to use Apache or nginx). Is there another way besides using Apache to create users automatically? Thanks, Hagai ___ 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/
[galaxy-dev] Get workflow info API problem
Hi,
I'm trying to use the API for showing workflow info which should be
something like:
/api/workflow/
But I'm getting the following error:
.../galaxy-dist/lib/galaxy/webapps/galaxy/api/workflows.py", line 80, in
show
label_name = step.tool_inputs['name']
TypeError: 'NoneType' object has no attribute '__getitem__'
Which came from the following commit, two years ago:
for step in latest_workflow.steps:
if step.type == 'data_input':
- inputs[step.id] = {'label':"Input Dataset", 'value':""}
+inputs[step.id] = {'label':step.tool_inputs['name'],
'value':""}
else:
pass
# Eventually, allow regular tool parameters to be inserted
and modified at runtime.
# p = step.get_required_parameters()
What is step.tool_inputs and why is it None on my instance?
(For my local installation, I changed to the following check: if step.type
== 'data_input' and step.tool_inputs is not None - so the else will be
triggered)
Thanks,
Hagai
___
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