Re: [galaxy-dev] Best practices for a local install of Galaxy for only 1 user on a Mac
Hi Paul, I have Galaxy running on a small Mac workstation. I have made a specific user, 'galaxy', for it. It is cleaner, but probably overkill for 1 person. Note also that you can install a daemon to start Galaxy automatically when your computer starts: https://bitbucket.org/galaxy/galaxy-central/src/d2d4b6ac2139f1623301990462a5e63b2952dcc1/contrib?at=default I don't think I have ever waited long enough to see the end of the unit tests. If some fail without any obvious reason (missing dependencies or what not), you should probably raise this issue on the Galaxy mailing list or bug tracker. Cheers, Florent On 15/06/13 08:54, Paul St. Amand wrote: I am trying to install Galaxy on a new iMac (i7, 32gb ram, OSX 10.8). Mostly the install worked and I can use my local install. However, about 25% of the functional tests failed for me. And about 4 of the unit tests failed for me. Also, I can't seem to install anything from the toolshed (logged in as Admin). Below is what I did to install. Can any Galaxy/Mac gurus out there please fix the errors in the below install list so that we can have a good idea of the best practices for installing Galaxy on a Mac running the latest version of OSX? Also, tips for installing all of the dependencies would be great too. Best practices for a local install of Galaxy for only 1 user on a Mac. For Galaxy on a Mac (OSX 10.8): To uninstall: delete galaxy-dist folder (should anything else be done??) To install Galaxy on a Mac (OSX 10.8): 1. Install Mercurial, download latest version from http://mercurial.selenic.com/mac/ and unzip and run installer. 2. Run the following in the terminal as a NON-root user (change pst to your user ID). (Is it better to create a galaxy user and install as user galaxy???) (Is it OK to use /Users/MacID/Applications as the install location, or is the home folder best??): % cd /Users/pst/Applications % hg clone https://bitbucket.org/galaxy/galaxy-dist/ % cd /Users/pst/Applications/galaxy-dist % hg update stable 3. After install, run this to start the server and create defaults, then Control-C to quit the server: % cd /Users/pst/Applications/galaxy-dist % sh run.sh % Ctrl-c in the terminal 4. Make the following changes to the universe_wsgi.ini file (found in /Users/pst/Applications/galaxy-dist/) using any text editor, save file as a UNIX text only file (TextWrangler works great for this) (What other changes should be made?). library_import_dir = /Users/pst/Documents/GalaxyDataFiles allow_library_path_paste = True admin_users = you...@yourlocation.com allow_user_dataset_purge = True debug = False use_interactive = False cleanup_job = onsuccess 5. Set Up Visualizations: % cd /Users/pst/Applications/galaxy-dist % cp datatypes_conf.xml.sample datatypes_conf.xml 6. Get wigToBigWig and bedGraphToBigWig from (http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/) and copy the files to the /Users/pst/Applications/galaxy-dist/ folder. 7. Set both files to be executable: % chmod +x /Users/pst/Applications/galaxy-dist/bedGraphToBigWig % chmod +x /Users/pst/Applications/galaxy-dist/wigToBigWig 8. Test installation with: % cd /Users/pst/Applications/galaxy-dist % sh run_functional_tests.sh 9. Check test output. The above command will output an html file called run_functional_tests.html (found in /Users/pst/Applications/galaxy-dist/) which contains all of the details of the test, along with additional information for failed tests. 10. Other tests: % cd /Users/pst/Applications/galaxy-dist % sh run_unit_tests.sh 11. Check test output. The above command outputs an html file called run_unit_tests.html (found in /Users/pst/Applications/galaxy-dist/) which contains all of the details of the test, along with additional information for failed tests. 12. Install dependencies?? To start the local Galaxy server: % cd /Users/pst/Applications/galaxy-dist % sh run.sh To use the local Galaxy server, enter this URL in your web browser: http://localhost:8080 To stop the Galaxy server, just hit Ctrl-c in the terminal window from which Galaxy is running. To see if new releases are available: % cd /Users/pst/Applications/galaxy-dist % hg incoming If no changes found then you are up to date. If changes are found, then add new versions with: % hg pull -u To update local galaxy: % cd /Users/pst/Applications/galaxy-dist % hg update stable ___ 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/ ___ 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:
Re: [galaxy-dev] Existing efforts to convert the QIIME pipeline to Galaxy?
Hi Amanda,
I would certainly be interested in using your helpful QIIME wrappers if
you put them on the Toolshed.
Best,
Florent
On 06/02/12 06:22, Amanda Zuzolo wrote:
Hello, all.
I have been working on getting the Qiime scripts into Galaxy as
mentioned before, and they are working with Qiime 1.3.0. I have edited
the wrapper file that Jim Johnson wrote to create more flexibility,
especially in cases where the tool looks for a specific file type
extension (for example, a .fna file), or where the tool normally
outputs something to the command line that is not normally picked up
in Galaxy.
So far, I have completely finished fixing the XML files to the latest
documentation for the entire Pick OTU process, Alpha Diversity, and
Beta Diversity, as well as other miscellaneous functions. Currently, I
am working on making scripts for jack-knifing functional. I determined
that it would be easier to get individual scripts functional, rather
than workflow scripts, since that allows the end-user to have more
control. Additionally, the workflow scripts can easily be recreated by
using Galaxy's workflows.
As far as the toolshed goes, I don't believe I know the ins and outs
yet, but I would be more than willing to learn if people would benefit
from having these versions in that repository.
2012/1/29 Jim Johnsonjohns...@umn.edu:
Pat,
That sounds great. Do one of you want to take ownership of the toolshed
repository?
At minimum, we should add developers to the list that can push changes.
Thanks,
JJ
On 1/28/12 9:37 AM, Gillevet Patrick wrote:
Jim et al
Amanda has most of the scripts working now and will be putting them up on
the toolshed.
She will be in touch as soon as the scripts are validated a couple of times
with different datasets.
cheers...
Pat
On Dec 29, 2011, at 3:02 PM, Jim Johnson wrote:
It is easiest to generate tools for galaxy when the applications or scripts
can take arbitrarily named input files and generate output to given path
names.
Input directories, output directories are very convenient on the command
line, but more of a challenge when crafting a galaxy tool.
That said, many applications require a wrapper script to work with in
galaxy.
Thank you for the consistent script_info[] help/usage syntax in the qiime
scripts, which enabled me to generate a skeleton galaxy tool_config file
for each qiime script.
I had some time last spring to work on integrating qiime into galaxy.
Unfortunately, I haven't had any time since to work on this.
I put those partial results on the Galaxy Tool Shed:
http://toolshed.g2.bx.psu.edu/
There's a continuing effort at George Mason University to incorporate qiime
into galaxy tools, so you may want to ask them what they need.
I started by generating galaxy tool_config files, e.g. align_seqs.xml, by
using python to get the script_info[] from the qiime script:
$ cat generate_tool_config.bash
#!/usr/bin/env bash
python $1 ${1%.*}.help
cat tool_template.txt | sed s/__TOOL_BINARY__/${1}/ | python -i $1 -h
${1%.*}.log
(I'll attach tool_template.txt )
This generated skeleton tool_config .xml files that I could then edit as
needed.
( http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax )
I originally was calling all qiime scripts from a tool wrapper:
qiime_wrapper.py
But, if a script can be called with any input filepaths and write its
results to any filepaths, and only writes to STDERR when it fails, then you
could call that script directly.
When should you use a tool_wrapper or call the qiime script directly?
Many of the qiime scripts could probably be called directly, especially if
it can be called with arbitary input/output file pathnames.
The reasons for using a tool wrapper may be if input/output needs to be
manipulated, moved, renamed in order to be used by the qiime script.
You'll also need a tool wrapper if the names or number of the output files
can not be determined from the parameter settings.
( http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files )
If your tool relies on a file ext to determine a format, you'll have to
rename the input.
( Galaxy dataset pathnames will look something like:
/your_galaxy_file_path/072/dataset_72931.dat )
The format/type of a dataset is stored in its metadata, so the tool_config
can use that information, especially if a script can take muliple
alternative input formats.
A tool_wrapper can also be used to manage the stdout or stderr from a
tool. Galaxy currently interprets any output on stderr as a failure.
A couple changes in galaxy should make somethings easier than when I first
attempted this:
- galaxy now accepts dataset requests with sub directories. (
https://bitbucket.org/galaxy/galaxy-central/issue/494/support-sub-dirs-in-extra_files_path-patch
)
That means that output HTML files with links into sub directories can be
left intact, with the html copied to the output dataset and the linked files
to its extra_files_path.
- if you know the pathname
Re: [galaxy-dev] amplicon reads(with errors)
Hi Bassam, Try Grinder, which is available from the Galaxy Toolshed at http://toolshed.g2.bx.psu.edu/. Regards, Florent On 30/12/11 04:23, Bassam Tork wrote: Dear All, Is there a way to generate 454 simulated amplicon reads with errors using galaxy. Happy New Year, Bassam Tork. ___ 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] [galaxy-user] Problem with new tool shed
Hi Greg, Thanks for the reply. I believe that how easy it is to write tools wrappers plays a big role for how widespread Galaxy becomes. I filed an issue at https://bitbucket.org/galaxy/galaxy-central/issue/670/better-support-for-multiple-outputs so that the issue is recorded. Best, Florent On 14/10/11 06:45, Greg Von Kuster wrote: Hello Forent, On Oct 13, 2011, at 2:48 AM, Florent Angly wrote: But maybe I need a little bit of guidance with this because the example shown, the user is given a _limited_ number of output datasets to choose from. The Grinder case seems simple: give the user a field where he can specify the number of output he wants, say, 2, 10, or 100 and produce as many datasets as needed. So, in theoutput section, the only reasonable way to process the output would be to have some sort of loop. Is this possible? This is not yet possible. This is something that has been desired for some time, but is not on our near-future plans for implementation. Thank you, Florent Greg Von Kuster Galaxy Development Team g...@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] [galaxy-user] Problem with new tool shed
Hi Greg,
Thank you for your help. Your suggestion worked like a charm!
I was expecting to see an error because I did not create the
../shed_tool/ folder that contains the tools installed from the shed,
but I was happy to see that it was automatically created.
I have a few additional comments and questions though:
1/ In the universe_wsgi.ini file, maybe the tool_config_file parameter
could be renamed to tool_config_files (plural) to indicate that it takes
a list of files.
2/ It seems like the Tools Search box cannot find newly installed tools.
However, after I restart Galaxy, it works as intended again.
3/ In the Grinder wrapper, I relied on installing the wrapper under a
specific folder: ./tools/ngs simulation/grinder. The new wrapper
installation procedure installs the tools in the ../shed_tools/ folder
and the admins can choose under what category the tool is to be placed.
This means that my Grinder wrapper fails since it does not know where to
find the scripts it needs. Is there a way to get the directory where a
tool is installed? Here is an excerpt of the Grinder wrapper so you can
better understand what I am trying to do. This wrapper first runs
Grinder and then moves its files (the number of files is hard to
determine ahead of time) to a place where Galaxy will find them (see the
wiki page
http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files under
section Number of Output datasets cannot be determined until tool run).
Thanks,
Florent
command
#set $tool_dir = os.path.join( os.path.abspath($__root_dir__),
'tools', 'ngs_simulation' )
#set $script1 = os.path.join( $tool_dir, 'stderr_wrapper.py' )
#set $script2 = os.path.join( $tool_dir,
'grinder_multiple_outputs.py' )
$script1
grinder
#if $reference_file.specify == builtin:
-reference_file ${ filter( lambda x: str( x[0] ) == str(
$reference_file.value ), $__app__.tool_data_tables[ 'all_fasta'
].get_fields() )[0][-1] }
#else if $reference_file.specify == uploaded:
-reference_file $reference_file.value
#end if
[...]
#if str($homopolymer_dist):
-homopolymer_dist $homopolymer_dist
#end if
#set $output_dir = $__new_file_path__
-output_dir $output_dir
#set $base_name = $output.id
-base_name $base_name
;
$script2 $output_dir $base_name
/command
On 04/10/11 22:55, Greg Von Kuster wrote:
Hello Florent,
Sorry for the confusion on this - we are preparing a new Galaxy distribution,
and the tool shed wiki has been written in preparation for it. The new
distribution will be available fairly soon, and the Galaxy News Brief will
include information about these new tool shed features. In any case, you have
already discovered that you can use in if you update your Galaxy instance to
the latest Galaxy development repository ( Galaxy central ).
The problem you see is most likely caused by your not having configured an
additional tool_config_file setting in your universe_wsgi.ini. Look for
something like following in your latest version of the universe_wsgi.ini.sample
that you got when you updated from Galaxy central.
# Locally installed tools and tools installed from tool sheds
tool_config_file = tool_conf.xml,shed_tool_conf.xml
If you add a new additional file name like shed_tool_conf.xml, you should not
have a problem installing from a tool shed. I'll have a fix for the bug you've
discovered shortly, but making this change will fix the behavior until then.
Let me know if you bump into any additional problems.
Thanks for finding this!
Greg Von Kuster
On Oct 4, 2011, at 2:53 AM, Florent Angly wrote:
Hi all,
I tried the latest stable version of Galaxy:
http://wiki.g2.bx.psu.edu/News%20Briefs/2011_08_30. This page has links to how
to use the new tool shed including how to automatically deploy tools from the
shed in a local Galaxy server.
The documentation mentioned some tool shed options available from the the admin
section of Galaxy but I could not locate these options in my instance of
galaxy. So my question is: Can one only take advantage of the tool deployment
from the shed in the development version of Galaxy? If so, I think the Tool
shed wiki should be more clear about this.
Then I tried the latest development version of Galaxy and could locate the tool shed deployment options. I attempted to install the Grinder wrapper
(http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=namewebapp=communityid=3d8312720a69a558f-deleted=Falseshow_item_checkboxes=falseasync=falseoperation=view_or_manage_repositoryf-free-text-search=grinderpage=1http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=namewebapp=communityid=3d8312720a69a558f-deleted=Falseshow_item_checkboxes=falseasync=falseoperation=view_or_manage_repositoryf-free-text-search=grinderpage=1)
but ran into an error that I am pasting below:
URL:
http://localhost:8080/admin
Re: [galaxy-dev] outputting different numbers of files based on variables?
Thanks for the pointer Ross. It was really useful. I also found more information about multiple output datasets on the wiki: http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files?highlight=%28dataset%29 I plan on writing a script that renames the output of the Grinder tool I am wrapping to a name that will work well with what Galaxy expects from multiple output datasets. Best, Florent On 15/09/11 18:44, Ross wrote: If you need every output as an item in your history, does the example in http://lists.bx.psu.edu/pipermail/galaxy-user/2009-September/000743.html help? Naming might be a wart. Otherwise the html datatype is really handy for throwing variegated output into a single history item page. It can look like FastQC eg. On Thu, Sep 15, 2011 at 5:47 PM, Florent Anglyflorent.an...@gmail.com wrote: Hi, I too would be interested in knowing how to handle tools that might generate multiple output files for the Grinder wrapper I am developing. Any news on this? Has a ticket been recorded? How about when the tool generate an number of files that cannot be determined from the values the user inputs in the form, or when you don't know what the files will be named. It seems like there should be generic way to loop through the files that were created by the tool in its working directory and decide what to do about them. Thanks, Florent On 27/08/11 10:22, Nikhil Joshi wrote: It seems that theconditional element can only be used WITHIN adata element in the outputs. But that won't do what I want. I know that you can useconditional in theinputs element in that way, but it will NOT work that way in theoutputs element. However, I have found a way to do what I want using thefilter element. I basically have all the outputs for both the single-end and paired-end reads, but I filter out the outputs based on whether the user chose single or paired end. If anyone has a better way to do it, I would love to know! - Nik. On Fri, Aug 26, 2011 at 4:26 PM, Duddy, Johnjdu...@illumina.com wrote: The BWA tool in NGS mapping does just what you want, just for inputs. The general idea is to use aconditional element and define your extra output in awhen block. John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.com From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nikhil Joshi Sent: Friday, August 26, 2011 3:57 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] outputting different numbers of files based on variables? Hi all, Is it possible to output a different number of files based on variables that the use has chosen? I have a program that will output different numbers of files based upon the input data. So, for example, if the user wants to use a single-end fastq file, the program outputs only one file, however, if the user chooses paired-end fastq files, it outputs three files. Is there any way to get that to work in just one tool? I could make separate tools for single vs. paired end, but I'd rather not. ___ 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] outputting different numbers of files based on variables?
Hi, I too would be interested in knowing how to handle tools that might generate multiple output files for the Grinder wrapper I am developing. Any news on this? Has a ticket been recorded? How about when the tool generate an number of files that cannot be determined from the values the user inputs in the form, or when you don't know what the files will be named. It seems like there should be generic way to loop through the files that were created by the tool in its working directory and decide what to do about them. Thanks, Florent On 27/08/11 10:22, Nikhil Joshi wrote: It seems that the conditional element can only be used WITHIN a data element in the outputs. But that won't do what I want. I know that you can use conditional in the inputs element in that way, but it will NOT work that way in the outputs element. However, I have found a way to do what I want using the filter element. I basically have all the outputs for both the single-end and paired-end reads, but I filter out the outputs based on whether the user chose single or paired end. If anyone has a better way to do it, I would love to know! - Nik. On Fri, Aug 26, 2011 at 4:26 PM, Duddy, John jdu...@illumina.com mailto:jdu...@illumina.com wrote: The BWA tool in NGS mapping does just what you want, just for inputs. The general idea is to use a conditional element and define your extra output in a when block. *John Duddy Sr. Staff Software Engineer Illumina, Inc. *9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 tel:858-736-3584 E-mail: jdu...@illumina.com mailto:jdu...@illumina.com *From:*galaxy-dev-boun...@lists.bx.psu.edu mailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu mailto:galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Nikhil Joshi *Sent:* Friday, August 26, 2011 3:57 PM *To:* galaxy-dev@lists.bx.psu.edu mailto:galaxy-dev@lists.bx.psu.edu *Subject:* [galaxy-dev] outputting different numbers of files based on variables? Hi all, Is it possible to output a different number of files based on variables that the use has chosen? I have a program that will output different numbers of files based upon the input data. So, for example, if the user wants to use a single-end fastq file, the program outputs only one file, however, if the user chooses paired-end fastq files, it outputs three files. Is there any way to get that to work in just one tool? I could make separate tools for single vs. paired end, but I'd rather not. - Nik. ___ 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] Fwd: Request for pulling the updated FASTQ (de-)interlacer tool
Hi Kanwei, I think we'll get more feedback once it when it is added to Galaxy. I have run small tests (included in the functional tests) and real large datasets and have had no issues with the scripts and wrappers. Regards, Florent On 27/05/11 18:49, Kanwei Li wrote: Has anyone on the list tried this patch? Feedback would be appreciated. Thanks, K On Fri, May 27, 2011 at 1:27 AM, Florent Angly florent.an...@gmail.com mailto:florent.an...@gmail.com wrote: Can anyone comment on my email please? Florent On 22/05/11 14:03, Florent Angly wrote: 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.an...@gmail.com mailto:florent.an...@gmail.com To: galaxy-dev@lists.bx.psu.edu mailto:galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu mailto:galaxy-dev@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 ___ 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] stdout and stderr
On 27/05/11 00:04, Peter Cock wrote: I regard fixing issue 325 as one of the top priorities in Galaxy Can't agree more with you Peter! This bug and other tool wrapper related bugs make it harder and more tedious to contribute tool wrappers. It's a big turn off for me. Florent ___ 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] Fwd: Request for pulling the updated FASTQ (de-)interlacer tool
Can anyone comment on my email please? Florent On 22/05/11 14:03, Florent Angly wrote: 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.an...@gmail.com To: galaxy-dev@lists.bx.psu.edu galaxy-dev@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 ___ 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] Fwd: Request for pulling the updated FASTQ (de-)interlacer tool
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.an...@gmail.com To: galaxy-dev@lists.bx.psu.edu galaxy-dev@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 ___ 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] Wrapper generator.
Hi Jeroen, The idea of having a tool to automatically generate Galaxy wrappers is attractive, and in some cases, possible. For example, I know that the tools in QIIME (http://qiime.sourceforge.net/) use some sort of argument declaration and a Python module to read it and deal with the command-line interface. This makes it possible to write a converter that would generate (or at least kickstart) Galaxy wrappers. I also have some Perl scripts that use the Getopt::Euclid module (http://search.cpan.org/dist/Getopt-Euclid/), which declares all the arguments taken by the program. I have been contemplating writing code that would convert the Getopt::Euclid specifications into a Galaxy wrapper. At the moment, though, there are quite a few outstanding irritating bugs in the Galaxy wrapper system that force you to use workarounds to get a working wrapper: https://bitbucket.org/galaxy/galaxy-central/issues?component=tools-configsort=id https://bitbucket.org/galaxy/galaxy-central/issues?component=tools-configsort=id. Needless to say that it would be easier to automated wrapper generation if these bugs were fixed. Regards, Florent On 14/05/11 00:03, J. F. J. Laros wrote: Dear Dave, This indeed sounds like an interesting alternative. I'll look into it. With kind regards, Jeroen. On Fri, May 13, 2011 at 01:48:12PM +, Dave Walton wrote: An alternative might be to have something like GenePattern has. It's not as seamless for the person who wants the wrapper as what's been suggested here, but it's easier than creating a lengthy XML file. GenePattern has an HTML Form interface for entering all the components of your tool, including the command-line you want to expose and the parameters you want to make available, and then it generates the back-end. There are definite down-sides to this. I've never tested what keeps the tool in GenePattern from letting you do destructive things. Dave On 5/13/11 9:41 AM, Peter Cockp.j.a.c...@googlemail.com wrote: On Fri, May 13, 2011 at 2:12 PM, J. F. J. Larosj.f.j.la...@lumc.nl wrote: Hi Pieter, Thanks for the reply, but from the looks of it, this is a way to incorporate webservice clients into galaxy. What I want is slightly different. I'm talking about adding a normal command line tool (an aligner for example) but I'm not willing to write a wrapper each time (the wrapper for BWA for example is 327 lines). If a computer readable description of the interface exists, this description can be used to generate a python wrapper. I mentioned WSDL because this also gives a description of an interface, but any equivalent description would of course be fine. Ideally, such a description is maintained by the developer of the tool in question. With kind regards, Jeroen. How many tools can you name that come with such a machine readable file describing their command line interface? I can think of only one - the EMBOSS tool suite and their ACD files (used internally by EMBOSS to generate the command line help, documentation, and do the command line option parsing). Unfortunately I don't think there is an easy answer - even if wrapping a tool where all the input and output formats are already supported in Galaxy. 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/ ___ 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] Special considerations for installing local instance of Galaxy on Mac OS X (10.6.7)?
Hi Jeff Some of these tools can be installed easily on Mac OS using MacPorts port search gnuplot Of course, you have to install MacPorts first. Florent On 23/04/11 01:25, Whyte, Jeffrey wrote: Hi Everyone, I'm having trouble getting some of the tools to work on my local installation of Galaxy on a Mac (OS X version 10.6.7). The instructions on the GetGalaxy wiki are clear, and I was able to download and install from the anonymous Mercurial repository. Galaxy starts up and runs just fine for tools like Get Data, FASTQ Groomer, and FASTQ Summary Statistics. The problems started when I try to run Graph/Data Display - Boxplot (GnuPlot). I get the error: An error occurred running this job:/bin/sh: gnuplot: command not found Error running gnuplot. The FASTX Barcode Splitter also gives me an error: An error occurred running this job:/Users/Me/galaxy-dist/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh: line 65: fastx_barcode_splitter.pl: command not found zcat: /Users/Me/galaxy-dist/database/files/000/dataset_10.dat.Z: No such file or directory sed: illegal opt I'm assuming these are Tool Dependency problems, although I have tried to install the OS X versions of GnuPlot and the FASTX Toolkit and still get errors. Are there any suggestions from users who are successfully running Galaxy on OS X? Thanks in advance, Jeff ___ 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] Special considerations for installing local instance of Galaxy on Mac OS X (10.6.7)?
Jeff, I haven't tried GnuPlot specifically in Galaxy, but all the applications that you install with MacPorts are installed under /opt/local/bin. I think that MacPorts adds this folder to your $PATH. So yes, Galaxy should be capable of finding any program that you installed through MacPorts. Florent On 24/04/11 12:22, Whyte, Jeffrey wrote: Hi Florent, I installed MacPorts this afternoon, but that was after I installed gnuplot (sudo make install). Have you found that gnuplot works in Galaxy if installed through MacPorts? Thanks for the suggestion. Jeff On Apr 23, 2011, at 7:03 PM, Florent Angly wrote: Hi Jeff Some of these tools can be installed easily on Mac OS using MacPorts port search gnuplot Of course, you have to install MacPorts first. Florent On 23/04/11 01:25, Whyte, Jeffrey wrote: Hi Everyone, I'm having trouble getting some of the tools to work on my local installation of Galaxy on a Mac (OS X version 10.6.7). The instructions on the GetGalaxy wiki are clear, and I was able to download and install from the anonymous Mercurial repository. Galaxy starts up and runs just fine for tools like Get Data, FASTQ Groomer, and FASTQ Summary Statistics. The problems started when I try to run Graph/Data Display - Boxplot (GnuPlot). I get the error: An error occurred running this job:/bin/sh: gnuplot: command not found Error running gnuplot. The FASTX Barcode Splitter also gives me an error: An error occurred running this job:/Users/Me/galaxy-dist/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh: line 65: fastx_barcode_splitter.pl: command not found zcat: /Users/Me/galaxy-dist/database/files/000/dataset_10.dat.Z: No such file or directory sed: illegal opt I'm assuming these are Tool Dependency problems, although I have tried to install the OS X versions of GnuPlot and the FASTX Toolkit and still get errors. Are there any suggestions from users who are successfully running Galaxy on OS X? Thanks in advance, Jeff ___ 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] Ratings on Tool Shed broken?
Hi Peter, I get the same error here. Florent On 06/04/11 01:50, Peter Cock wrote: Hi all, I had wondered why none of the tools on the Galaxy Tool Shed had a rating, and had assumed it was just that so far no-one had bothered. I have a new theory, it doesn't work? I just viewed Brad's BAM to BigWig tool, clicked on Tool Actions then Rate Tool, and got: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Can anyone reproduce this? I've tried a couple of other tools and the same thing happens. Thanks, 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/ ___ 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] [galaxy-user] Galaxy does not find my executables
I understand that it is best to flow with the logic of the underlying OS and not too make too many platform-dependent assumptions about what files should be read. Perhaps, it seems like the best way to go would be to have a setting in universe_wsgi.ini to specify a file to read additional environment settings from? For example, in my case, I would add a line like: source_environment_from = '/Users/galaxy/.profile' Best, Florent On 16/02/11 05:58, Nate Coraor wrote: Hi Florent, et. al., I've moved the discussion over to galaxy-dev since it pertains to local instances. Florent Angly wrote: Indeed, this workaround works! Thank you. I added these lines to the beginning of my run.sh: PATH=/opt/local/bin:/opt/local/sbin:$PATH export $PATH Now, Galaxy can find Grinder, Velvet, etc Could Galaxy detect and use ~/.profile automatically if it exists? Alternatively, maybe there should be a place in the configuration file universe_wsgi.ini to specify which file to read environment variables from? Is it worth filing an enhancement request in the bug tracker? Unfortunately, this is really more of an issue with the way shells are designed. Galaxy can't make too many assumptions about how you want the environment to be set up, especially since it's run under a variety of shells. What's going to happen is dependent entirely upon how the parent shell to Galaxy is started. By default if invoked in non-login, non-interactive mode (which would likely be the case for most managed startup methods like launchd, rc scripts, etc.), bash will not read *any* startup files. This behavior can be changed by specifying the path to a file to be sourced in the $BASH_ENV environment variable in the calling environment. However, when bash is called as 'sh', even $BASH_ENV is not available. For more details, see the INVOCATION section of the bash(1) man page. Since the public site runs on Solaris, we solve this by setting $PATH and any other relevant variables within SMF. Similar methods should work (setting the $PATH in an init script or in the LaunchDaemon plist) for other startup methods. Although modifying run.sh as mentioned does work, modifications could conflict with future changes from the upstream source repository. --nate P.S. I'll add a plug for zsh - its invocation is much less confusing and ~/.zshenv is *always* read regardless of invocation. Again, thanks for the help. Florent ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
