:
--SS_lib_type $inputs.library_type
#end if
Or, this might work too:
#if $inputs.library_type != None:
--SS_lib_type $inputs.library_type
#end if
(This does seem to be a bug in the trinity wrapper)
Peter
___
in universewgsi.ini - but this is not really general enough.
For now however, you do generally have to tweak the wrappers
as you have done to edit any hard coded thread setting :(
Peter
___
Please keep all replies on the list by using &quo
red
database will be updated, and the production server will probably
stop working. That's assuming there are not other issues before
that...
(If you are talking about running two version-locked production
servers, then perhaps there is precedent with load balancing
systems which might be worth
sue 393: Can't use checkbox (boolean) with conditional parameters
https://bitbucket.org/galaxy/galaxy-central/issue/393/ [DEAD LINK]
I can't find the matching entry on Trello though... so maybe
only open issues were migrated?
The workaround was to use a select with two options.
Peter
_
On Wed, Mar 20, 2013 at 3:47 PM, Peter Cock wrote:
> On Wed, Mar 20, 2013 at 3:43 PM, Raj Ayyampalayam wrote:
>> Hi Guys,
>>
>> Thanks for the quick response. I installed the latest blast datatypes from
>> the toolshed and that fixed the issue.
>
> Great - thank
for this confusion. There was talk some time ago about merging both
> attributes to work correctly in all cases, but this was never done.
>
> --nate
Is this still the case?
I'm guessing this is what Raj was alluding to with the BLAST+ wrapper
for makeblastdb which creates a compo
On Wed, Mar 20, 2013 at 3:43 PM, Raj Ayyampalayam wrote:
> Hi Guys,
>
> Thanks for the quick response. I installed the latest blast datatypes from
> the toolshed and that fixed the issue.
Great - thanks for letting us know so promptly.
> Peter, can you also fix the $outfile.extr
On Wed, Mar 20, 2013 at 1:55 PM, Peter Cock wrote:
> On Wed, Mar 20, 2013 at 1:52 PM, Nicola Soranzo wrote:
>> Il giorno mer, 20/03/2013 alle 12.41 +0000, Peter Cock ha scritto:
>>>
>>> The patch just removes the MetadataElement call - is that wise?
>>
>&
On Wed, Mar 20, 2013 at 1:52 PM, Nicola Soranzo wrote:
> Il giorno mer, 20/03/2013 alle 12.41 +0000, Peter Cock ha scritto:
>>
>> The patch just removes the MetadataElement call - is that wise?
>
> Hi Peter,
> my question instead is, what are they for? With '
https://bitbucket.org/nsoranzo/peterjc-galaxy-central-tools2/commits/35163cbc6c694f598ed1a1875353c58b275e2423
>
> I have sent a pull request to Peter (the maintainer), hopefully he will
> release soon a new version of blast_datatypes with this fix.
>
> Best,
> Nicola
The patch ju
your XML file though a standard XML validator (there
are lots online), which will spot any silly things like broken tags.
Second, when you restart Galaxy, I like to do this by running the
run.sh script at the terminal so I can see the output on screen.
Look for any error message
On Tue, Mar 19, 2013 at 1:43 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> Please feel free to edit the ToolConfigSyntax page if you get a chance.
> Unfortunately I have my hands full with just the tool shed wiki, and it is
> not possible for me to get time to keep the e
On Tue, Mar 19, 2013 at 1:15 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> You are correct. A tool dependency definition is associated with a tool via
> the tool config's tag set. The combination of name, version
> and type is used to associated a tool with a tool dependency.
l's XML
should reference the package somehow? If so, then the
wiki needs updating as it only describes python-module
and binary as requirement types:
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Thanks,
Peter
___
Please keep
On Mon, Mar 18, 2013 at 4:52 PM, Dannon Baker wrote:
> Björn, Peter, and John,
>
> Thanks for finding and fixing this issue -- the fix has been merged
> into galaxy-central and should be available with the next distribution
> release currently scheduled for April 1. We'
doesn't
allow no column to be picked. It occurred to me a simple UI idea
would be to include a dummy 'No column' entry in the drop down
before column 1, column 2, etc.
Would that be acceptable?
Peter
___
Please keep all repl
r (overall it will only slow jobs
down). I suspect it is more suited to local institute clusters
which are not typically under full load - where it helps by
making each individual job complete more quickly.
Perhaps there is a case for one
On Sun, Mar 17, 2013 at 3:40 PM, Björn Grüning
wrote:
> Am Sonntag, den 17.03.2013, 15:26 + schrieb Peter Cock:
>> On Sun, Mar 17, 2013 at 3:13 PM, Björn Grüning wrote:
>> > Hi all,
>> >
>> > can anyone confirm that the parallelism features is not working
Which hg revision are you on from galaxy-central? It was
working for me last time I tested, but my setup isn't fully
up-to-date with the development repository.
(This makes a nice change from it being me reporting that
something on the trunk broke the parallelism
On Fri, Mar 15, 2013 at 2:51 PM, John Chilton wrote:
> Hey Peter,
>
> I wonder if it is better to ask the user what type they would like to
> select and then have the input param inside the conditional.
That is doable now, but I'm not sure it is optimal for usability.
> My
On Wed, Apr 18, 2012 at 12:01 PM, Peter Cock wrote:
> Dear all,
>
> I've looked over the wiki and as far as I can see, 'when' tags used inside
> 'conditional' tags only work on another input variable's values.
>
> I would like to be able to do i
Hello all,
Either I made a typo in some old README files, or the old
URL for the Tool Shed http://community.g2.bx.psu.edu/ has
stopped working. Could this redirect to the current Tool Shed
address http://toolshed.g2.bx.psu.edu/ please?
Thanks,
Peter
c repo?
Thanks,
Peter
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On Mon, Feb 4, 2013 at 6:14 PM, Peter Cock wrote:
> On Mon, Feb 4, 2013 at 5:43 PM, Luobin Yang wrote:
>> Hi, Peter,
>>
>> What difficulties did you see to include psi-blast and phi-blast when you
>> were working on the other programs in the NCBI+ suite? I would be
On Tue, Mar 5, 2013 at 10:08 AM, Ira Cooke wrote:
> Hi Peter,
>
> The problem is that I have multiple repositories in my repository_dependency
> file ... but they need to be installed in a specific order. I can't seem to
> get
> galaxy to install them in the correct order
instance, i.e. http://toolshed.g2.bx.psu.edu/ here):
http://wiki.galaxyproject.org/DefiningRepositoryDependencies
Peter
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On Mon, Mar 4, 2013 at 3:16 PM, John Chilton wrote:
> Hi Alex and Peter,
>
> I appreciate the comments, but I am not going to keep talking about
> this issue here, I consider the issue closed. The Galaxy team has
> spoken clearly on this topic. They have accepted dozens of my
On Fri, Mar 1, 2013 at 2:55 PM, Peter Cock wrote:
> Hello all,
>
> Re: BitBucket Issue 538 - Admin action to reload ".loc" files without
> restarting Galaxy
> https://trello.com/card/538-admin-action-to-reload-loc-files-without-restarting-galaxy/506338ce32ae458f6d15e4b3
l
https://trello.com/c/325AXIEr
Jeremy's idea mentions the special case of a unique dataset
collection object for paired-end reads - well if that was defined
using the existing core Galaxy functionality as a 'pairedfastq'
composite datatype (made of two FASTQ files), then could we
use &#
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
>
--
Peter Waltman, Ph.D.
pwalt...@ucsc.edu
617.347.1876
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oved or copied - simply
that imports work relative to the location of the Python script.
In much the same way, you should be able to get the relative
path to your template files by using the location of the script
(and not the current working direc
nate: http://wiki.galaxyproject.org/Events/GCC2013
Regards,
Peter
-- Forwarded message --
From: Jonathan Rocher
Date: Wed, Feb 27, 2013 at 10:17 PM
Subject: [Numpy-discussion] [ANN] SciPy2013: Call for abstracts
To: SciPy Users List ,
numfo...@googlegroups.com, Discussion of Numeri
(re)loading loc files on demand
rather than at startup.
Do the Galaxy team have any plans in this area?
Thanks,
Peter
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*.*rev*(*p1*)**,* addlistdelta*(*addlist*,* delta*)**)
*
Module mercurial.manifest:*124* in addlistdelta
>>
>> <http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d#>
addlist*[*start*:*end*]* *=* array*.*array*(*'c'*,* content*)*
*TypeError: ar
er message).
Apologies if I missed something, thanks again
Best wishes, Peter
On 27/02/13 18:33, Jeremy Goecks wrote:
Thanks Peter. I've added your patch to the Trello card tracking incorporation
of community contributions to the Bowtie wrapper:
https://trello.com/c/TdYxdbkm
Best,
J.
end ..." isn't commented,
so the integer conversion fails causing the error you saw. The patch
just traps for the integer conversion error.
HTH, best wishes, Peter
On 27/02/13 19:16, greg wrote:
Thanks Peter. I'm running it now after applying your fix.
Any idea what the problem was
local tool).
I've attached patches to the tool in case they're any use to you.
(As an aside and more generally: I'm not sure how to manage these local
customisations in the longer term - what do other people on this list do?)
HTH, best wishes, Peter
On 25/02/13 11:29, Alexande
# "bad" line instead
+fields[0] = "#%s" % fields[0]
out.write( '\t'.join( fields ) )
out.close()
I'm intending to feed this back to the tool authors once things got a
bit quieter here.
HTH, best wishes
Peter
On 26/02/13 15:52, gr
On Mon, Feb 25, 2013 at 8:02 PM, Samuel Lampa wrote:
> Hi, thanks for the quick reply!
>
>
> On 02/25/2013 08:39 PM, Peter Cock wrote:
>>>
>>> I realize that when the master script ("run.R" in my case) is run, it
>>> will
>>> >not find
out the path of the master R script,
and from that compute the path to the child R scripts. I guess
you can do this in R using commandArgs().
For future reference, queries about writing tools and extending
Galaxy should go to the galaxy-dev list (CC'd), not galaxy-users.
Peter
_
On Wed, Feb 20, 2013 at 2:57 PM, Peter Cock wrote:
> Bumping one of my old queries again, with some more use-cases at the end,
>
> On Wed, Aug 10, 2011 at 11:28 AM, Peter Cock
> wrote:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-August/006350.html
>
>
> Hi al
On Fri, Feb 22, 2013 at 2:55 PM, Nicola Soranzo wrote:
> Il giorno mar, 19/02/2013 alle 20.38 +0000, Peter Cock ha scritto:
>> The current minimal implementation you sent me for BLAST+
>> would be an excellent start. Things like data type sniffers etc
>> would be a nice to
on other tool sheds - and in
particularly the main tool shed at Penn State which I see
having a hub-like role. But right now, that doesn't work.
Is this a short term limitation (since cross-Tool Shed
dependencies are bound to be more complex to support),
or a deliberate policy?
Thanks,
Peter
_
other configurable options which have changed from
v2.3.5 to v2.5. Please read the blast2go.loc.sample for
details.
If you need any guidance on this, I will try to advise by
email, and make clarifications to the documentation if
required.
Regards,
Peter
On Thu, Feb 21, 2013 at 7:46 PM, Greg Von Kuster wrote:
> Hello Peter,
>
> This issue should now be corrected on both Galaxy tool sheds.
>
> Thanks very much,
>
> Greg Von Kuster
Looks good - thanks Greg!
Peter
___
Pl
On Thu, Feb 21, 2013 at 6:12 PM, Carlos Borroto
wrote:
> On Wed, Feb 20, 2013 at 9:57 AM, Peter Cock wrote:
>> [*] This is one reason why I've just switched the default BLAST+
>> output from the standard 12 column output to the extended 24
>> column output in v0.0.1
em sounds like a cookie path issue to me,
I had something similar when I added second public Galaxy
to our server (in my case, a live on and a dev one).
Peter
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in your m
On Wed, Feb 20, 2013 at 11:13 PM, James Taylor wrote:
> Peter, I quite like this idea, and I think it might be possible to do as a
> simple extension to the validator framework. Basically, a flag indicating
> that failing a certain validation would be able to be considered a warning
>
ust
the main tool overview page.
Thanks,
Peter
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On Tue, Feb 19, 2013 at 12:06 PM, Peter Cock wrote:
> On Tue, Feb 19, 2013 at 11:39 AM, Greg Von Kuster wrote:
>> On Feb 19, 2013, at 5:10 AM, Peter Cock wrote:
>>
>> Yes, the complete directory hierarchy and content of the original
>> repository revision is prese
tool
options). More generally, a warning might be desirable
only if certain options are used together.
Even stricter, for some tools it would be useful to show
an error message with particular option combinations,
and refuse to submit the job.
Any thoughts?
Peter
Bumping one of my old queries again, with some more use-cases at the end,
On Wed, Aug 10, 2011 at 11:28 AM, Peter Cock wrote:
> Bumping this old query:
>
> On Mon, Nov 22, 2010 at 10:11 AM, Peter wrote:
>> On Fri, Nov 19, 2010 at 12:20 PM, Peter wrote:
>>> Hi all,
>&
mmed over the instructions here, but would like to look
at a couple of real examples to make sure I've understood:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-February/013434.html
Are there any good examples of 3rd party Galaxy datatypes
defining conversion like this?
Thanks,
Peter
_
On Tue, Feb 19, 2013 at 6:45 PM, Nicola Soranzo wrote:
> Il giorno mar, 19/02/2013 alle 14.15 +0000, Peter Cock ha scritto:
>> On Tue, Feb 19, 2013 at 2:00 PM, James Taylor wrote:
>> > On Tue, Feb 19, 2013 at 6:32 AM, Peter Cock wrote:
>> >>I think it could make
On Tue, Feb 19, 2013 at 5:26 PM, Nate Coraor wrote:
> On Feb 19, 2013, at 12:18 PM, Peter Cock wrote:
> Nate wrote:
>>> Hi Peter,
>>>
>>> This is due to the annoying way in which Mercurial handles symlinks. We're
>>> going to graft the changeset
On Tue, Feb 19, 2013 at 5:08 PM, Nate Coraor wrote:
> On Feb 19, 2013, at 11:23 AM, Peter Cock wrote:
>
>> Hi all,
>>
>> I've got an hg puzzle, can anyone on the Galaxy team explain the
>> cause of this and what action I can take to avoid it?
>>
>> S
e/Makefile' traverses symbolic link
'static/june_2007_style'
I was actually trying to checkout one of my own branches, having
setup the .hg/hgrc to include a link to my own fork on bitbucket.
Thanks!
Peter
___
Please keep all rep
?
One solution might be automatic functional categories: tool shed
repositories which define a format, or define a tool for the user,
or define a dependency for use by other tools, etc
Thanks,
Peter
___
Please keep all replies on the list by
On Tue, Feb 19, 2013 at 2:00 PM, James Taylor wrote:
> On Tue, Feb 19, 2013 at 6:32 AM, Peter Cock wrote:
>> Would a pull request implementing this be acceptable?
>
> Yes. My understanding is that ASN is a completely flexible metaformat,
> like XML, and so should be under e
On Tue, Feb 19, 2013 at 11:39 AM, Greg Von Kuster wrote:
> On Feb 19, 2013, at 5:10 AM, Peter Cock wrote:
>
> Yes, the complete directory hierarchy and content of the original
> repository revision is preserved when it installed into Galaxy.
>
>> Based on a sample
c.
I see this as a clear analogy to the assorted XML file formats
in existence - defined in Galaxy as subclasses of the core
XML format included with the Galaxy core.
Would a pull request implementing this be acceptable?
Peter
P.S. Does anyone know an authoritative source for the MIME
types u
On Sat, Feb 16, 2013 at 9:41 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> Thanks for your thoughts on this. I've created the following Trello card for
> this enhancement.
>
> https://trello.com/card/galaxy-tool-enhancement-to-accommodate-repository-install-dir/506338ce32ae4
On Tuesday, February 19, 2013, Derrick Lin wrote:
> Thanks Peter,
>
> Our data is backup and we are planning to shutdown the galaxy for moving
> data to the new place, change the file_path value in universe config, then
> start the galaxy again.
>
> My only concern is if
On Fri, Feb 15, 2013 at 6:10 PM, Nicola Soranzo wrote:
>Peter wrote:
>>
>> It seems to have confused the bitbucket page a little, but I have
>> checked in your initial wrapper to my development repository (I
>> use the tools branch):
>> https://bitbucket.o
On Fri, Feb 15, 2013 at 4:57 PM, Greg Von Kuster wrote:
>
> On Feb 15, 2013, at 11:45 AM, Peter Cock wrote:
>> Actually for the example I am working on, the motif.py script would be
>> the tool executable, called from motif.xml like this:
>>
>> motif.py $fasta_f
f.xml).
>>>>
>>>> Perhaps I can just put my data file next to the script and XML file, in
>>>> which case it is easy for the script to locate? But I assumed that
>>>> Galaxy best practice would be to use the tool-data folder somehow...
>>>
pt to locate? But I assumed that
>> Galaxy best practice would be to use the tool-data folder somehow...
>>
>> Thanks,
>>
>> Peter
>
> The current implementation places your motif.dat data file in the
> repository installation directory, and tools that are prop
omething?
Usecase: Tool comes with a simple datafile (e.g. defining a search motif,
say motif.dat) which is used by a script (say motif.py) via a normal
Galaxy tool XML file (say motif.xml).
Perhaps I can just put my data file next to the script and XML file, in
which case it is easy for the script
time (and stop Galaxy of
course).
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-February/008383.html
Peter
On Thursday, February 14, 2013, Derrick Lin wrote:
> Hi Shantanu,
>
> We are facing the same situation that migrating galaxy dataset to a new
> location is needed. I am wond
On Mon, Feb 11, 2013 at 5:16 PM, Peter Cock wrote:
>>> However, this is already functional enough to start sharing
>>> direct links. Once this goes live, you'll have to brief the
>>> whoever writes the new tool alerts for Twitter to use it :)
>
> I look fo
On Mon, Feb 11, 2013 at 5:01 PM, Greg Von Kuster wrote:
> Hello Peter,
>
> In addition to the fixes I've commented on inline below, I've also added a
> new rout for specified repository revisions. So the following citable URLs
> are now supported in the test to
On Mon, Feb 11, 2013 at 1:54 PM, Dave Bouvier wrote:
> Peter,
>
> It looks like you have two dashes in your -sid option, whereas the parser
> expects just one.
>
>--Dave B.
Doh, thank you!
$ ./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools
...
FAILED (er
On Fri, Feb 8, 2013 at 4:30 PM, Nicola Soranzo wrote:
> Il giorno mer, 06/02/2013 alle 20.01 +0100, Nicola Soranzo ha scritto:
>> Hi Peter,
>> I added these file formats mostly as placeholders for a future
>> implementation. Now I have changed a bit the tool by removing accl
On Wed, Nov 3, 2010 at 11:48 AM, Peter wrote:
> On Tue, Nov 2, 2010 at 1:57 PM, Nate Coraor wrote:
>>
>> Peter wrote:
>>> Hi,
>>>
>>> I'm trying to use run_functional_tests.sh to run all the tests
>>> for a section (group of tools). I&#x
On Tue, Feb 5, 2013 at 4:28 PM, Luobin Yang wrote:
> Hi, Peter,
>
> You are right, I thought there was already a datatype defined for PSSM, but
> it turned out there isn't one yet. I attached a draft tool configuration
> file for psiblast, it was based on the blastp config
> On Feb 8, 2013, at 7:54 AM, Peter Cock wrote:
>
>> Hi all,
>>
>> I've been reading http://wiki.galaxyproject.org/ToolShedToolFeatures
>> and focused on the example of EMBOSS where the tool definitions
>> depend on the data type definitions. Here the
y for the 'blastxml' format (etc) - so
what happens when these three repositories don't all request the
same revision of the blast_datatypes repository?
What I'm using for now is:
http://toolshed.g2.bx.psu.edu";
name="blast_datatype
On Sat, Feb 2, 2013 at 1:56 PM, Peter Cock wrote:
> On Sat, Feb 2, 2013 at 12:46 AM, Greg Von Kuster wrote:
>> Hello Peter,
>>
>> I've added an enhanced version of your implementation for
>> citable URLS in the tool shed to change set revision
>> 8720:e27d0
Galaxy display
> other image formats like ps and pcx?
>
> Thanks,
> Luobin
I would guess this is possible but only if those other image types are
first defined in Galaxy as new datatypes (with sensible MIME type
values).
Peter
___
Ple
lit and merge
methods in lib/galaxy/datatypes/*.py). Some other relevant Python code
is in lib/galaxy/jobs/splitters/*.py
Peter
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filed on
Trello? http://galaxyproject.org/trello (I couldn't find it myself).
Peter
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other
groups. Fixing a non-core Galaxy tool may not be quite what your lecturer
had in mind, so do check ;)
Peter
On Wednesday, February 6, 2013, Matthew Paul wrote:
> Dear Galaxy Project community,
>
> I am working with a group of students at College of Charleston
> of Sout
On Mon, Feb 4, 2013 at 7:32 PM, Peter Cock wrote:
>
>
> On Monday, February 4, 2013, Luobin Yang wrote:
>>
>> Hi, Peter,
>>
>> Thanks for pointing them out!
>>
>> The phi-blast and psi-blast actually share the same binary, both use the
>> psiblas
On Monday, February 4, 2013, Luobin Yang wrote:
> Hi, Peter,
>
> Thanks for pointing them out!
>
> The phi-blast and psi-blast actually share the same binary, both use the
> psiblast program in the NCBI BLAST+ tools. When the option -phi_pattern is
> used, then it doe
On Mon, Feb 4, 2013 at 5:43 PM, Luobin Yang wrote:
> Hi, Peter,
>
> What difficulties did you see to include psi-blast and phi-blast when you
> were working on the other programs in the NCBI+ suite? I would be interested
> in creating a tool configuration file for each of these
most of the key NCBI BLAST+ standalone tools now, but not yet
psiblast or rpsblast.
Peter
P.S. When you said web-interface, did you mean to the NCBI online
server? As far as I know there are no Galaxy interfaces to that - just
for the standalone NC
On Sat, Feb 2, 2013 at 12:46 AM, Greg Von Kuster wrote:
> Hello Peter,
>
> I've added an enhanced version of your implementation for
> citable URLS in the tool shed to change set revision
> 8720:e27d0dd12752. This is currently running on the test
> tool shed, and v
On Fri, Feb 1, 2013 at 3:48 PM, Prasun Dutta wrote:
> Hi Peter,
>
> Unfortunately, I am not an advanced developer in python. Although, I have
> 'Cygwin' in my system. Any heads up on that will be greatly appreciated?
>
Cygwin is a useful system for running Unix/Linux
ws) Laptop to connect to the
public Galaxy at http://usegalaxy.org
Peter
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On Thursday, January 31, 2013, Greg Von Kuster wrote:
> Hi Peter,
>
> Thanks for the update and your contributions. Would you like me to
> continue with the work you've started, or would you like to continue
> yourself? I'll try to fit this in this week if you wa
On Thu, Jan 31, 2013 at 4:51 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> All of the tool-shed related required files will be automatically generated
> from the
> samples when you start your tool shed server as of change set
> 8708:2a34f751c32c.
> In the past, all of these sa
On Tue, Jan 29, 2013 at 4:44 PM, Peter Cock wrote:
> On Tue, Jan 29, 2013 at 4:17 PM, Greg Von Kuster wrote:
>> Hi Peter,
>>
>> The tool shed source is mostly in the following places.
>>
>> ~/lib/galaxy/webapps/community/
>> /lib/galaxy/tool_shed/
>>
On Thu, Jan 31, 2013 at 2:40 PM, Peter Cock wrote:
> 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 bitb
achi-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/Extra
cases, the search system is much more user friendly.
You have a special case wanting a blank entry in the list, there may
be a better way to handle that. One idea might be to use a caption
like instead of an empty string?
Peter
___
Please
ly
> ;-) ) 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
___
ad the input directory as a zip file without Galaxy decompressing it.
Have you looked at a composite datatype instead, where the files are
stored on disk decompressed?
http://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes
Peter
_
On Tue, Jan 29, 2013 at 4:17 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> The tool shed source is mostly in the following places.
>
> ~/lib/galaxy/webapps/community/
> /lib/galaxy/tool_shed/
> /lib/galaxy/util/shed_util_common.py
> /lib/galaxy/util/shed_util.py
>
On Tue, Jan 29, 2013 at 4:04 PM, Peter Cock wrote:
>
> I was wondering about taking a look at this to see how hard it would
> be - but my first query is where is the ToolShed source code?
>
I think I've found it, in the main repository under the slightly misleading
name of comm
or the ToolShed entry:
http://toolshed.g2.bx.psu.edu/repository/peterjc/mira_assembler
Thanks,
Peter
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