- galaxy-dev - lists.galaxyproject.org

How to use the API when using a proxy server
by Anthonius deBoer 01 Feb '13

01 Feb '13

Hi, I am trying to use the API with my galaxy server running behind a proxy server. How do I pass username/password information to the API so it can actually run? If I use the regular API calls I get a access denied... Thanks Thon

3 4

install Galaxy in Windows (URGENT)
by Prasun Dutta 01 Feb '13

01 Feb '13

Hi, I have Windows Vista and 8 in two separate laptops. I need to install a local version of Galaxy server in both the systems. I am unable to understand or follow the instructions given in your website (http://wiki.galaxyproject.org/Admin/Get%20Galaxy) Could you kindly help me or just explain me stepwise how to install it in my system? Regards, Prasun Dutta MSc (Bioinformatics) School of Biological Sciences University of Edinburgh, UK

3 4

loading file into local galaxy for first time
by Hakeem Almabrazi 01 Feb '13

01 Feb '13

Hi, I just finished installed a local galaxy. I tried to load a simple small fasta file using Load Data and it is still showing as Queued (Blue). It should not take it that much to load. SO I assumed I have some issues in my installation. Can someone tell me what could ne the issue? Or how to go about debugging it? By the way, where the logs in galaxy get stores at? Appreciate your help....

1 2

install reference genome Bwa and Bowtie!
by Hakeem Almabrazi 01 Feb '13

01 Feb '13

Hi, I just installed Galaxy in local Centos Vm. I did my best to get everything working ( I think). I followed the instructions in this Wiki (http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup) to install reference genomes for the tools Bwa and Bowtie. Here is what I did in details: 1. I installed all the software and added them to the PATH and everything seems to be working. 2. Then I created the indices as explained. 3. I put all the indices in the same recommended directory structure and gave all access rights to the Galaxy user which runs the Galaxy server. 4. I created the loc files (bowtie_indices.loc and bowtie_indices_color.loc and bwa_index.loc) and populate them with the recommended contents) and place them in ~/tool_data/ folder. 5. I copied the xml and py files from this location and put them into ~/tools/sr_mapping/.... https://bitbucket.org/galaxy/galaxy-dist/src/da9d740fce31/tools/sr_mapping This step was not mentioned in the instruction but I thought this might be the cause. 6. I restarted the server. Once I select NGS:Mapping tool and Bwa or Bowtie I do not see the reference genome in the list. Can someone tell me what I missed or how to go about debugging it? I appreciate any kind of help....

2 5

February 2013 Galaxy Update
by Dave Clements 01 Feb '13

01 Feb '13

1 0

How do I allow a large group of users to RUN my workflow without them having to make a local copy
by Anthonius deBoer 01 Feb '13

01 Feb '13

Hi, I am trying to build some workflows for people that are part of a group and I want to share that workflow with them, so that they can run the workflow without having to make a local copy for them self. It seems I can only share a workflow in that manner with an individual, and not with a group... Am I reading that correctly? It seems strange not to be able to share workflows with groups if you can share them with individual users.. I also have to know the exact username (email) for each user, rather than being able to choose it from a list... Is there any reason for this or is just underdeveloped? Thanks Thon

3 2

Error loading a BAM file -- dataset needs grooming
by Maureen J. Donlin 01 Feb '13

01 Feb '13

Hi, I tried to load a BAM file into our local instance of Galaxy but get the following error. I had preloaded the genome to which it was aligned and the bai file. Do I have to load these using a different method and the file upload? Thanks, Maureen Traceback error: Traceback (most recent call last): File "/work/apps/galaxy/tools/data_source/upload.py", line 384, in <module> __main__() File "/work/apps/galaxy/tools/data_source/upload.py", line 373, in __main__ add_file( dataset, registry, json_file, output_path ) File "/work/apps/galaxy/tools/data_source/upload.py", line 312, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/work/apps/galaxy/lib/galaxy/datatypes/binary.py", line 113, in dataset_content_needs_grooming version = self._get_samtools_version() File "/work/apps/galaxy/lib/galaxy/datatypes/binary.py", line 97, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib64/python2.6/subprocess.py", line 639, in __init__ errread, errwrite) File "/usr/lib64/python2.6/subprocess.py", line 1228, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory -- Maureen J. Donlin, Ph.D. Research Associate Professor Dept. of Biochemistry & Molecular Biology Dept. of Molecular Microbiology & Immunology Saint Louis University School of Medicine 507 Doisy Research Center Office: 314-977-8858 Cell: 314-750-2345

2 2

How to call a cgi web page in a galaxy folder from a script?
by Zinonas Antoniou 01 Feb '13

01 Feb '13

Hello, Now I have a web page (cgi) in a server like www.example.com/myexample.py I want to have the myexample.py file under a galaxy folder. Then, how will I call it inside a script in galaxy? Thank you in advance, Zinon

2 2

Patch for RepeatMasker.xml for RepeatMasker 3.3.0
by Guest, Simon 01 Feb '13

01 Feb '13

Dear Galaxians, We are using Galaxy with RepeatMasker 3.3.0. I don't know whether that is the expected version, as I can't find any statement about what is required in the Galaxy tool dependencies for RepeatMasker. Anyway, when a job is submitted with no repeats, RepeatMasker 3.3.0 doesn't create the various output and summary files (.tbl, .out.gff, .out.html, .masked). This causes the Galaxy job to fail with an error message that scares the end user. I attach a patch to handle this case, by touch'ing these files before trying to copy them. Now such jobs succeed with empty output. I think this is clearer, and certainly less scary. Is there a better mechanism for me to contribute such fixes other than posting patches on this list? cheers, Simon ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

3 2

Re: [galaxy-dev] Best way to work with one directory and many files as 1 input
by Pierre Pericard 01 Feb '13

01 Feb '13

Hi Christos, Yes, I would be very interested by your modified file. I'm forwarding to the mailing-list so this bug can be listed. Thanks, Pierre Pierre Pericard IE CDD - Projet Peptisan Service Informatique et Bio-informatique (SIB) Station Biologique de Roscoff CNRS - UPMC Place Georges Teissier CS 90074 29688 ROSCOFF CEDEX FRANCE Tel : (+33) 2 98 29 56 46 http://abims.sb-roscoff.fr/ Le 01/02/2013 00:34, chriskannas(a)gmail.com a écrit : > Hi, > > I'm working on the same thing, having a composite dataset with many files in many sub-folders. > > Well during the development & testing of the tool that uses this composite datatype, I found out that Galaxy does not handle correctly sub-dirs, it works pretty good with files but if it finds a sub-dir then the copy messes it up. > > To be more specific it uses shutil.copy without checking if it is file or directory, when coping dirs it has to use shutil.copytree. > > I managed to make our local Galaxy installation to handle them quite ok with some modifications in method DiskObjectStor.update_from_file(...) located in lib/galaxy/objectstore/__init__.py > > I can send you a copy of the file I've modified. > > Regards, > Christos > > ------ > > Christos Kannas > Researcher > Ph.D Student > > e-Health Laboratory > Dept. Computer Science, > University of Cyprus > > <quote author='Pierre Pericard'> > Ok, thanks a lot, I'll try and get back to the mailing list if other > problems seem to occur. > > Pierre. > > > Pierre Pericard > IE CDD - Projet Peptisan > > Service Informatique et Bio-informatique (SIB) > Station Biologique de Roscoff > CNRS-UPMC > Place Georges Teissier > CS 90074 > 29688 Roscoff CEDEX > FRANCE > http://abims.sb-roscoff.fr/ > > Le 30/01/2013 11:45, Ross a écrit : >> I'd suggest: >> 1) Make your new datatype a subclass of Html - it's a subclass of >> composite that contains an HTML document as the object's native >> display - so it can inform users what's there. >> >> 2) When constructing these new things, pass the file_path of the Html >> (composite) dataset subclass to your wrapper on the command line >> >> 3) Your wrapper code can construct any arbitrary structure as long as >> it's rooted in that directory - Galaxy stores it without any fuss. The >> wrapper should also populate the Html file itself with nicely >> laid annotation for the user to check out. >> >> 4) The key is that all tools that take this new datatype as input must >> know how to decode this structure - they must be passed the >> $input.extra_files_path which gives them that same path root. >> >> 5) Yes, it's odd and annoying that it's extra_files_path for >> files_path. Go figure. >> >> 6) grep extra_files tools/*.xml to find some examples - I think the >> velvetg one uses a complex subdirectory structure - but it doesn't >> really matter - as long as your tools know how to deal with it, it's >> just a directory to Galaxy! >> I hope all this helps... >> >> >> On Wed, Jan 30, 2013 at 8:22 PM, Pierre Pericard >> <pierre.pericard(a)sb-roscoff.fr <mailto:pierre.pericard@sb-roscoff.fr>> >> wrote: >> >> In that case, could anyone point me to an example of a Composite >> Datatype which could accept as input an unknown number of files in >> an unknown number of directories. I can't seem to understand how >> that would work based on the wiki. >> >> But maybe are we anticipating a near functionality of Galaxy. >> There were talks about changing the way Galaxy handle zip files, >> is it still on the table ? >> >> Thank in advance for any help, >> >> Pierre >> >> >> >> Pierre Pericard >> IE CDD - Projet Peptisan >> >> Service Informatique et Bio-informatique (SIB) >> Station Biologique de Roscoff >> CNRS-UPMC >> Place Georges Teissier >> CS 90074 >> 29688 Roscoff CEDEX >> FRANCE >> http://abims.sb-roscoff.fr/ >> >> Le 29/01/2013 18:04, Peter Cock a écrit : >> >> On Tue, Jan 29, 2013 at 4:58 PM, Pierre Pericard >> <pierre.pericard(a)sb-roscoff.fr >> <mailto:pierre.pericard@sb-roscoff.fr>> wrote: >> >> If I'm not mistaking, Composite Datatypes allow for only >> one directory, >> whereas we need to keep a constant directory structure >> with 2 or more >> sub-directories containing our input files. >> >> I'm not sure if that is true - the example of HTML output with >> images >> comes to mind as a common use-case where subfolder(s) would be >> expected. I've only had limited first hand experience with >> Galaxy's >> composite datatypes myself though. >> >> We have no way to change these tools behavior (obviously >> not Galaxy-friendly >> ;-) ) and therefore need to maintain this structure in the >> job working >> directory. >> >> Perhaps a tool wrapper could create a dummy folder using symlinks >> (faster and less wasted disk than copying files), but that >> isn't ideal. >> >> Peter >> >> >> ___________________________________________________________ >> > > ___________________________________________________________ > 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/ > </quote> > Quoted from: > http://dev.list.galaxyproject.org/Best-way-to-work-with-one-directory-and-m…

1 0