June 2011 - galaxy-dev - lists.galaxyproject.org

Patch to add twobit type
by Peter van Heusden 13 Jun '11

13 Jun '11

Hi everyone I've been using the twobit datatype as generated by faToTwoBit (part of Jim Kent's BLAT package) and read by bx-python (bx.seq.twobit). So here's a patch to add the twobit datatype to Galaxy. Peter

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Generating hashed-id of datasets outside galaxy
by Assaf Gordon 11 Jun '11

11 Jun '11

Hi, I recently needed to generate the dataset's hashed-id from a reporting script outside galaxy (a script that reads Galaxy database directly). Here's how to generate the hashed-id from perl and postgres, hope it would save you some time if you ever need it. (The python code to do the same is of course already in galaxy, see "encode_id" in galaxy/web/security/__init__.py). === Perl === #!/usr/bin/perl use strict; use warnings; use Crypt::Blowfish; my $id = shift or die "Usage: $0 HISTORY-DATASET-ASSOCIATION-ID\n"; die "Invalid ID ($id)\n" unless $id =~ /^\d+$/; ## This is the same value of "id_secret" from your "universe_wsgi.ini" file my $glx_id_secret = "My_Secret_Code" ; my $cipher = new Crypt::Blowfish ( $glx_id_secret ); my $padded_str_id = ( '!' x (8- length($id) % 8 ) ). $id ; my $ciphertext = $cipher->encrypt($padded_str_id); my $hash_id = unpack('H*', $ciphertext ) ; print $hash_id, "\n"; =============== === PostgreqSQL === CREATE FUNCTION galaxy_encode_id(HISTORY_DATASET_ASSOCIATION_ID integer, GALAXY_ID_SECRET bytea) RETURNS text AS $$ SELECT substring( encode( encrypt( decode(lpad('', 8-length($1)%8,'!')||$1, 'escape'), $2, 'bf'), 'hex') from 1 for 16 ) ; $$ LANGUAGE SQL; =========== (For postgreSQL, you'll need the "postgres-contrib" package, and run the "pgcrypto.sql" script). This allows you to run a SQL command that automatically creates the preview URL, e.g.: Show all datasets belonging to me that are bigger than 1GB, and add a "preview" URL link, so I can quickly check them out: ============ select hda.name, history.name, dataset.file_size, 'http://rave.cshl.edu/galaxy/datasets/' || galaxy_encode_id(hda.id, 'my_secret_id') || '/display?preview=True' as PREVIEW_URL from history_dataset_association hda, galaxy_user, history, dataset where history.user_id = galaxy_user.id AND hda.history_id = history.id AND hda.dataset_id = dataset.id AND hda.deleted = false AND galaxy_user.email ='gordon(a)cshl.edu' AND dataset.file_size > 1000000000 ============ -gordon

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Re: [galaxy-dev] [galaxy-user] Videos online of the Galaxy community conference 2011
by Dave Clements 10 Jun '11

10 Jun '11

Hello all, I would like to second (or third!) the thanks to NBIC for sponsoring the videotaping of all talks and for making them available online. We had several requests for this and we were delighted when NBIC provided the funds to make this happen. I have updated the conference talks page (http://wiki.g2.bx.psu.edu/GCC2011) to link to the videos for each talk. Thanks again. I think this will be a great resource. Dave C. On Fri, Jun 10, 2011 at 9:41 AM, Marc van Driel <marc.van.driel(a)nbic.nl>wrote: > Hello all, > > > > Thanks to all speakers and participants of the Galaxy Community Conference > 2011. You made this an excellent meeting. > > *Videos* are now available at > > > > http://vimeo.com/nbic > > > > *Feedback: > *Please give your feedback on the meeting to the Galaxy team. A short, > one-page survey is at > > > > http://bit.ly/ltUnyj > > > This information will be used when planning future Galaxy events. > > > > Best, > > > > Marc > > _____________________________________________________ > > Marc A. van Driel (PhD) > > Netherlands Bioinformatics Centre > > Coordinator Bioinformatics > > > > 260 NBIC > > P.O. Box 9101 > > 6500 HB Nijmegen > > > > Tel. +31 (0)24 36 19500 (NBIC Office) > > Tel. +31 (0)24 36 13306 (Direct) > > Tel. +31 (0)6 24448612 (Mobile) > > Skype: marc.van.driel > > Fax. +31 (0)24 89 01 798 > > E.mail marc.van.driel(a)nbic.nl > > http://www.nbic.nl > > _____________________________________________________ > > > > ___________________________________________________________ > 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/ > -- http://getgalaxy.org http://usegalaxy.org/

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Fwd: Request for pulling the updated FASTQ (de-)interlacer tool
by Florent Angly 10 Jun '11

10 Jun '11

Let me know if you have any questions about this. Thanks, Florent -------- Original Message -------- Subject: Request for pulling the updated FASTQ (de-)interlacer tool Date: Tue, 17 May 2011 17:47:13 +1000 From: Florent Angly <florent.angly(a)gmail.com> To: galaxy-dev(a)lists.bx.psu.edu <galaxy-dev(a)lists.bx.psu.edu> Dear Galaxy team, Please consider pulling these changes I made to the interlacer/de-interlacer tools into the main Galaxy repository: https://bitbucket.org/fangly/galaxy-central/changeset/7f7ec8f05d36 While the tools were handling mate pairs fine, I now added the ability to also keep single reads (reads that miss their mate) in a separate file. The functional tests were updated and pass. Thanks, Florent

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UnicodeDecodeError
by Sarah Diehl 10 Jun '11

10 Jun '11

Hello everybody, currently I have some trouble with the following kind of error: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 155: ordinal not in range(128) We have encountered it twice now. The first time it was related to a shared library, which could not be opened anymore because of this error. So we deleted the library and set it up again. The second time it was related to a workflow. Clicking on "Run" caused this error to appear, while editing still worked. This time I saved the error message and you can find it attached to this mail. The cause of the error was a < sign in a renaming step inside the workflow (the < was part of the new name). After removing the < everything worked again. However, when using the < in a history item, it works without a problem. Unfortunately I cannot reproduce the error currently on my machine. The computer that caused it was a Mac. Should we just try to avoid any special characters or is this actually a bug which could be fixed? Best regards, Sarah

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use external authentication bare username as email address without appending any email domain
by Leandro Hermida 10 Jun '11

10 Jun '11

Hi, Is it possible to tell Galaxy to use the bare username passed back by external authentication as the email address without appending any domain? It seems to complain if it isn't in email address format and asks you to set up a domain to append in universe.wsgi. I would like to use the bare username as the email address since it works fine as an email address in for example any Active Directory-based organization and also in many non-academic organizations it is preferred not to use the email addresses as the ID. thanks in advance, Leandro

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Recommended method to pull from ToolShed ?
by Assaf Gordon 09 Jun '11

09 Jun '11

Hi, with the new ToolShed inplace, and support for cloning/pulling tools directly: What's the recommend way to organize the repositories ? For example, I want to use Peter's Venn tool: hg clone http://toolshed.g2.bx.psu.edu/repos/peterjc/venn_list If I clone, I get the following folder hierarchy: venn_list -> tools -> plotting -> xml/py . So I can't directly clone into the <galaxy>/tools folder. Even if I could (somehow skipping the "venn_list" directory), cloning multiple tools would override the ".hg" folder of each other. so is it still a manual process of cloning to a temporary directory, then manually copy the files to the <galaxy>/tools folder ? or am I missing something ? being able to automagically "pull -u" tools from the toolshed would be really cool. thanks, -gordon

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Fwd: [galaxy-user] Galaxy tool error report from johnwu@ibms.sinica.edu.tw
by Jeremy Goecks 09 Jun '11

09 Jun '11

John, Questions about local installs are best directed to galaxy-dev, so I've moved the question to this list. >> While executing cuffcompare, I encountered this error message: >> >> Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' >> >> I was practicing RNA-seq analysis steps on newly installed galaxy to test if i could easily analyze my data. >> >> I could run cufflinks and cuffdiff through galaxy, but i'm unable to run cuffcompare. >> >> how should i solve this problem? >> >> thanks a lot! A recent change set has made Cuffcompare compatible with v1.0.3: https://bitbucket.org/galaxy/galaxy-central/changeset/f4b98c453389 You'll need to update your Galaxy instance with this change set for Cuffcompare to work; also note that the change set is in galaxy-central, not galaxy-dist. Best, J.

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ValueError: numpy.dtype does not appear to be the correct type object
by Peter Cock 09 Jun '11

09 Jun '11

Hi all, I just updated our development machine to the latest from galaxy-central, and it broke: $ ./run.sh Traceback (most recent call last): File "/home/pjcock/repositories/galaxy-central/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/home/pjcock/repositories/galaxy-central/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/home/pjcock/repositories/galaxy-central/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/home/pjcock/repositories/galaxy-central/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/home/pjcock/repositories/galaxy-central/lib/galaxy/visualization/tracks/data_providers.py", line 16, in <module> from bx.arrays.array_tree import FileArrayTreeDict File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object I checked I had the latest numpy and bx_python egg files by removing them, Galaxy downloaded the same ones: bx_python-0.7.0_494c2d1d68b3-py2.6-linux-x86_64-ucs2.egg numpy-1.6.0-py2.6-linux-x86_64-ucs2.egg This is a 64 bit Linux machine. Any ideas what might be wrong? I'm guessing some Pyrex or Cython extension module in an egg file needs recompiling. Note there is a system level install of NumPy 1.4.1 on this machine, but I believe the egg is used in preference? Peter

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bowtie on localgalaxy
by Arun Selvam 09 Jun '11

09 Jun '11

Hi, I am new to galaxy, I just downloaded and installed galaxy on my MAC system. I also download bowtie , and it is working perfectly on the command line. But am not able to see the bowtie option under mapping in the galaxy menu. Do I have to do another modifications like move into particular folder or create some files or set path ? Could anyone please help me on this ? Thank you Arun

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