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

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

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

uploading big file on local Galaxy
by stefano cardinale 01 Feb '13

01 Feb '13

Hi, I have installed Galaxy on our local server, which is up and running. I have a very big file (>5Gb) which I want to upload and I don't want to use the upload option but rather sftp or use FileZilla, where should I transfer the file to show up in my History? thanks! stefano Cardinale Stefano Postdoctoral researcher Arkin Lab Department of Bioengineering Energy Biosciences Building 2151 Berkeley Way 94720 - Berkeley

3 2

how to sftp a file on a local instance of Galaxy
by stefano cardinale 31 Jan '13

31 Jan '13

Hi, I have installed Galaxy on our local server, which is up and running. I have a very big file (>5Gb) which I want to upload and I don't want to use the upload option but rather sftp or use FileZilla, where should I transfer the file to show up in my History? thanks! stefano Cardinale Stefano Postdoctoral researcher Arkin Lab Department of Bioengineering Energy Biosciences Building 2151 Berkeley Way 94720 - Berkeley

2 1

Re: [galaxy-dev] Best way to work with one directory and many files as 1 input (Pierre Pericard)
by Christos Kannas 31 Jan '13

31 Jan '13

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 <http://www.medinfo.cs.ucy.ac.cy/> kannas.christos(a)ucy.ac.cy kannas.christos(a)cs.ucy.ac.cy chriskannas(a)gmail.com

1 0

FW: install reference genome Bwa and Bowtie!
by Hakeem Almabrazi 31 Jan '13

31 Jan '13

-----Original Message----- From: Hakeem Almabrazi Sent: Thursday, January 31, 2013 7:54 AM To: 'Carlos Borroto' Subject: RE: [galaxy-dev] install reference genome Bwa and Bowtie! Thank you Carlos for your help, I was sure that was not the case (all in tabs). Here is my bwa_indices.loc file look like ##################### #bwaReference /usr/local/galaxy_data/hg19/bwa/ hg19_reference_genome /usr/local/galaxy_data/hg19/bwa/hg19_reference_genome.fasta ####################### The same issue is happening with bowtie. Is there anything I need to do somewhere else in the system (DB, configuration files etc) i.e in ~ tool-data/shared/ucsc/builds.txt file. Regards, Hakeem -----Original Message----- From: Carlos Borroto [mailto:carlos.borroto@gmail.com] Sent: Wednesday, January 30, 2013 10:22 PM To: Hakeem Almabrazi Subject: Re: [galaxy-dev] install reference genome Bwa and Bowtie! On Wed, Jan 30, 2013 at 7:19 PM, Hakeem Almabrazi <halmabrazi(a)idtdna.com> wrote: > 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. Most of the time I run into this issue this is the step where I'm messing up. Double check you are using TABs (not spaces) to separate values in these files. Also check you have only one TAB between values, some of the examples have more than one for pretty formatting but that will cause the configuration not to work. Hope it helps, Carlos

2 4

Re: [galaxy-dev] python version
by Dannon Baker 31 Jan '13

31 Jan '13

Hi Kathryn, Hopefully instructions here should help you out: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use… I've also cc'd the galaxy-dev list as that's the best place to ask questions like this instead of emailing team members directly. Using the list, you'll reach a larger audience who may be able to help you and at the same time the answer to your question can benefit others. Let me know if you have any more trouble, -Dannon Sun, Wenping [USA] wrote: Hi Dannon, The python at my server version is 2.4. I have installed python 2.7 and set link as well as path based on the guide. However, the default python version still remain unchanged and galaxy would not run. Would you mind providing some help on this? Thank you very much, Kathryn

1 0

Running a local tool shed - teething trouble
by Peter Cock 31 Jan '13

31 Jan '13

Hi all, I was hoping to make some enhancements to the ToolShed, so first I need to be able to run my own ToolShed locally: http://wiki.galaxyproject.org/HostingALocalToolShed I have the latest code for bitbucket for galaxy-central: $ hg heads default changeset: 9117:04e221996871 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Jan 30 16:47:20 2013 -0500 summary: Dont' assume a complex repository dependency was properly defined. The following cryptic error is not helpful: $ sh run_community.sh Command 'serve' not known (you may need to run setup.py egg_info) No commands registered. Have you installed Paste Script? (try running python setup.py develop) I then noticed that there was no community_wsgi.ini file, and tried using a copy of the sample: $ cp community_wsgi.ini.sample community_wsgi.ini $ sh run_community.sh (runs with no output, finished in 3s) Does it make sense to generate community_wsgi.ini automatically? Or give an explicit error if it is missing? Looking at the log file, I have a Python depenancy issue here: $ more community_webapp.log ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/builds.txt' ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/publicbuilds.txt' ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ensembl/builds.txt' ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ncbi/builds.txt' WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Traceback (most recent call last): File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/webapps/community/buildapp.py", line 56, in app_factory from galaxy.webapps.community.app import UniverseApplication File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/webapps/community/app.py", line 2, in <module> from galaxy import tools File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/tools/__init__.py", line 36, in <module> import galaxy.util.shed_util_common File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/util/shed_util_common.py", line 27, in <module> eggs.require( 'markupsafe' ) File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/eggs/__init__.py", line 413, in require return pkg_resources.working_set.require( req_str ) File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/pkg_resources.py", line 666, in require needed = self.resolve(parse_requirements(requirements)) File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here DistributionNotFound: markupsafe Removing PID file community_webapp.pid Should this work under Mac OS X? I suspect there are some eggs missing on the Galaxy site which would be needed: $ python2.6 ./scripts/fetch_eggs.py Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: ssh (a dependent egg of Fabric) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 37, in <module> c.resolve() # Only fetch eggs required by the config File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Volumes/Hitachi-3TB-mirrored/repositories/galaxy-central/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Regards, Peter

2 5

sort the list of users while impersonating a user.
by Luobin Yang 30 Jan '13

30 Jan '13

Hi, The list of users is not sorted when I try to impersonate a user, this is very inconvenient because of the large number of users in the system, is there a quick way to have users sorted ? Thanks, Luobin

1 1