February 2013 - galaxy-dev - lists.galaxyproject.org

Fwd: Custom Cheetah filters?
by Ross 12 Feb '13

12 Feb '13

Hi Russell, There may be a better way, but this works for me in the Toolfactory to create space and special character free names? <param name="foo" type="text" value="" label="Foo"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"/> </sanitizer> </param> On Wed, Feb 13, 2013 at 11:22 AM, Smithies, Russell < Russell.Smithies(a)agresearch.co.nz> wrote: > I want to add a filter to strip whitespace and newlines from a text input > box so I can pipe the sanitized string to a command.**** > > Documentation is a bit sparse (and my Python a bit basic) so does anyone > have an example?**** > > Perhaps there’s a better way of doing it – regex maybe?**** > > ** ** > > Any ideas?**** > > ** ** > > Thanx,**** > > ** ** > > --Russell**** > > -- **** > > ** >

2 1

tool integration SOAPdenovo
by Jorge Andrade 12 Feb '13

12 Feb '13

Dear all, Is there a repository where I can finnd SOAPdenovo tool wrappers for Galaxy? I would like to install this tool in our local Galaxy server. Thanks, Jorge

2 1

Regarding bug card #572 (Trello) and Galaxy Public Server
by Matthew Paul 12 Feb '13

12 Feb '13

Regarding this issue ( https://trello.com/card/filter-and-sort-select-tool-not-dealing-with-specia… ): No bug is apparent when using an up-to-date local instance of Galaxy (local history on Trello card). However, when using the Galaxy public server the bug is apparent (regular expressions are not registered). So we have come to a few conjectures, 1) The bug has already been fixed in the newest version of Galaxy or 2) Somehow, instantiating the public server is the source of the error (which is unlikely). If one can elucidate any misconceptions (especially about the current version of the Galaxy public server) that we may have that would be great. We would like to resolve this bug. Thank You

2 1

Re: [galaxy-dev] Extract genomic DNA job error
by Jeremy Goecks 12 Feb '13

12 Feb '13

> So we did the following: > Downloaded the data > Added the paths to .loc file > restarted galaxy > > We still are getting the following error: > > 2: Extract Genomic DNA on data 1 > empty > format: fasta, database: hg19 > 56 warnings, 1st is: Chromosome by name 'chr22' was not found for build 'hg19'. Skipped 56 invalid lines, 1st is #1, "chr22 23487552 23487738 NM_004914_cds_0_0_chr22_23487553_f 0 +" My guess is that you .loc file is not set up correctly; you'll need to make sure that there are tab characters—not spaces—separating the columns. If that's not the case, try finding the command line in the galaxy log and running it from the command line (make sure to prepend the command with 'PYTHONPATH=./lib' to get needed Galaxy libraries) and adding debugging statements to see why you twobit file isn't being found. Line 200 of extract_genomic_dna.py may be the key failure point. Finally, please keep all replies on the mailing list for community purposes. Thanks, J.

1 0

Upload file : auto-detect based on file extension ?
by David Angot 12 Feb '13

12 Feb '13

Hi, We are using a proprietary file format in some of our tools. I successfully added a new data type, but what I would like to do is to use the auto-detect when uploading the file, just based on the extension of the file. My guess is I have to override the sniff() in the datatype class, and test for the extension ? Somethinkg like that : if file.endswith('.extension123'): ... But how do I get the original filename when it was uploaded ? Thanks, -- David

2 1

Re: [galaxy-dev] [galaxy-user] Why SGE needed for galaxy ?
by Dannon Baker 12 Feb '13

12 Feb '13

The workers don't need their own copy of galaxy installed, but a shared filesystem is a requirement for galaxy (in any cluster environment -- see the galaxy wiki for more http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster) Cloudman handles managing NFS for you and sharing the galaxy/tools/index/data volumes. In order for workers to communicate with the master instance, they'll need the cloudman installation as well, so you should use the same image. Now that I've answered that, I'm not sure I totally understand your proposed installation yet, but if you're suggesting bypassing cloudman for installation on a private cloud it should be possible. You'd want the master instance up full time running as the galaxy front end, dispatching jobs to a separate cluster managed by SGE/PBS/whatever. Basically the standard cluster configuration outlined in the wiki above, but you'd want your worker nodes automatically configured to mount the shared directories and join the PBS/SGE queue so they could handle jobs. Depending on what type of private cloud you're working with, it might be easier to just see if you can get cloudman to work :) Lastly, I swapped this message to galaxy-dev since it's about installation nuts and bolts. -Dannon On Feb 8, 2013, at 3:02 AM, Zeeshan Ali Shah <zashah(a)pdc.kth.se> wrote: > Dear Enis, thanks for reply and being you as cloudman developer it is good to see you in the list . > > Q2: On Workers node we need galaxy installed with its shared directories ? like galaxyindices , galaxydata > Q3: For a private cloud setup do you prefare to have a master image with cloudman and galaxy and use the same image for workers as well ? or worker images can be vanilla OS ? > > > BR > > Zeeshan > > On W6-Feb 7, 2013, at 11:50 PM, Enis Afgan wrote: > >> Hi Zeeshan, >> In order to gain from the scalability of the cloud, SGE does need to run. However, CloudMan sets all that up and manages it going forward. >> >> Enis >> >> >> On Fri, Feb 8, 2013 at 8:59 AM, Zeeshan Ali Shah <zashah(a)pdc.kth.se> wrote: >> Hi, >> >> It seems that cloud man need SGE for scaling . Does SGE need also when run cloud on private cloud ? >> >> Zeeshan >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

4 6

report server failing - lib/galaxy/webapps/reports/config.py does not have attribute sentry_dsn
by Jim Johnson 11 Feb '13

11 Feb '13

File '/home/galaxy/gx/prod/galaxy/database/compiled_templates/reports/base/base_panels.mako.py', line 68 in render_body __M_writer(unicode(self.javascripts())) File '/home/galaxy/gx/prod/galaxy/database/compiled_templates/reports/webapps/reports/index.mako.py', line 104 in render_javascripts __M_writer(unicode(parent.javascripts())) File '/home/galaxy/gx/prod/galaxy/database/compiled_templates/reports/base/base_panels.mako.py', line 301 in render_javascripts if app.config.sentry_dsn: AttributeError: 'Configuration' object has no attribute 'sentry_dsn' I patched in this as a temporary work around: $ hg diff -r 8182 lib/galaxy/webapps/reports/config.py diff -r ec51a727a497 lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py Thu Nov 01 23:25:39 2012 -0700 +++ b/lib/galaxy/webapps/reports/config.py Mon Feb 11 19:06:30 2013 -0600 @@ -45,6 +45,8 @@ global_conf_parser = ConfigParser.ConfigParser() if global_conf and "__file__" in global_conf: global_conf_parser.read(global_conf['__file__']) + # Error logging with sentry + self.sentry_dsn = kwargs.get( 'sentry_dsn', None ) def get( self, key, default ): return self.config_dict.get( key, default ) def check( self ):

2 1

Search for toolname from toolshed in workflow editor does not work?
by Thon de Boer 11 Feb '13

11 Feb '13

Hi, It seems that the workflow editor does not know how to search for tools that are in the toolshed. The regular toolsearch in the main Analysis window has no problem finding "reorder Sam/BAM" in picard if I search there, but in the workflow editor it seems to only be able to search for tools that are installed outside the toolshed. Do I need to turn this on somewhere or is this just a bug? Thanks Thon

2 1

Nice 'citable' URLs for Galaxy Tool Shed repositories
by Peter Cock 11 Feb '13

11 Feb '13

Dear all, Something I am conscious of every time I have directed someone to a tool or wrapper on the Galaxy Tool Shed is the lack of nice stable URLs. The current frame based design hinders this - and as a result I usually just have to give the ToolShed URL and tell them what to search for. This problem is particularly acute for citing a tool shed entry, where a nice URL would be far better. I appreciate moving away from the current frame interface is a lot of work - although what Jeremy Goecks wrote last week suggests that is a long term goal: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-January/012792.html I would like something similar to the repository URL, but for the ToolShed interface. e.g. The repository view for my MIRA wrapper: http://toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler Perhaps is the short-term what could be done is to enhance the repository view, and include links between this and the current "Tool Shed" frame based page? That way we can share a nice URL like http://toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler to direct someone to a resource in the Tool Shed? e.g. (1) When viewing an entry on the "Tool Shed", include a prominent link to the repository URL (perhaps even with social media links like tweet or share this to emphasise this is the best URL to share). (2) In the header for each repo (perhaps in place of the current Mercuiral logo?) have a link to the "Tool Shed" frameset for the tool being viewed. Thanks, Peter

5 22

run_functional_tests.sh -sid option
by Peter 11 Feb '13

11 Feb '13

Hi, I'm trying to use run_functional_tests.sh to run all the tests for a section (group of tools). I've read the output from: ./run_functional_tests.sh help For example, from the tools_conf.xml.sample we have <section name="ENCODE Tools" id="EncodeTools"> <tool file="encode/gencode_partition.xml" /> <tool file="encode/random_intervals.xml" /> </section> And looking at these tools' XML files, <tool id="gencode_partition1" name="Gencode Partition"> and: <tool id="random_intervals1" name="Random Intervals"> I'd like to run the functional tests for the ENCODE tools, Using the switch for an individual tool id (-id) works, ./run_functional_tests.sh -id gencode_partition1 ... Ran 1 test in 22.302s ... and so does this (well, it say the tool doesn't have any tests which is true in this example): ./run_functional_tests.sh -id random_intervals1 ... Ran 1 test in 0.027s ... However, I also tried using the section id switch (-sid), ./run_functional_tests.sh -sid EncodeTools ... Ran 0 tests in 0.000s ... I also tried using the section name, /run_functional_tests.sh -sid "ENCODE Tools" Is this (-sid not working) a known issue, or am I using it wrong? Thanks, Peter

4 5