Re: [galaxy-dev] Error Setting Up Local Galaxy Server

Hi, Kevin. Yes. that looks like an interesting error message which might have been caused because Galaxy currently requires a version of Python such as 2.7.8 (2.6+ will work fine) but it will not run under the newest Python v3 releases (eg Python 3.4.1) (You may also have encountered a bug in that

Re: [galaxy-dev] Dependencies within dependencies

Hi Christophe - there's a trello card for this at https://trello.com/c/ClgcV0Sn - upvote and add your experiences please? On Wed, Sep 17, 2014 at 8:01 AM, Christophe Antoniewski < christophe.antoniew...@snv.jussieu.fr> wrote: > I am trying to move the package_r_3_0_3 repository owned by devteam

Re: [galaxy-dev] tool for STAR RNA-seq aligner

v] tool for STAR RNA-seq aligner > > Hi David, > > yes there is inital code in the https://testtoolshed.g2.bx.psu.edu/. I > think Ross has done some work on it. > The main problem with Star is that is needs special indices (and a lot of > it) and it would be great to offer data manager

Re: [galaxy-dev] tool for STAR RNA-seq aligner

is a pain - best to write a data manager. Ross Lazarus Head, Computational Biology, Baker IDI, Melbourne, Australia Pubs: http://scholar.google.com/citations?hl=en&user=UCUuEM4J On Thu, Sep 25, 2014 at 6:39 AM, David Hoover wrote: > Why didn't I see these before? Hmm, I thoug

Re: [galaxy-dev] tool for STAR RNA-seq aligner

where you learned about this deprecation ? On Thu, Sep 25, 2014 at 10:41 PM, David Hoover wrote: > Ross, > > About the index files: It is way easier to have pre-built index files. > However, when running a 2-pass STAR run, a user will need to generate their > own reference index fil

Re: [galaxy-dev] Can't change working directory during tool dependency installation

You might need to specify multiple command lines in a single shell action - separated by ; like: cd foo; perl foo bah; more something; cleanup Otherwise you might just find yourself back in the temp installation directory after each separate action Ross Lazarus Head, Computational Biology, Baker

Re: [galaxy-dev] strange issue with .RData files

Rdata is binary and serialises R objects so I sure hope you don't have to peek inside - probably needs most of an R environment - like rpy or something. A binary header signature magic number would be ideal - I checked a few saved rdata files lying around here and all seemed to start with the follo

Re: [galaxy-dev] Unable to add R package dependency to tool_dependencies.xml

Hi, Bruno. As Björn points out, cross-toolshed dependencies aren't currently supported but exporting (eg) package_r_3_1_1 as a capsule (make sure to include ALL dependencies) from one toolshed and importing that capsule into your own local toolshed brings all the sub-dependent packages so they exis

Re: [galaxy-dev] strange issue with .RData files

ts to find a reliable magic number, it will be difficult to stop a user uploading an rdata file called "foo.fasta" - unpredictable things may happen. On Thu, Nov 6, 2014 at 8:35 PM, Lukasse, Pieter wrote: > Hi Ross, > > > > I also found the following information: >

Re: [galaxy-dev] dataset_*_file directory being compied to file_path when running fastqc

gt; Bioinformatics – Intern > > icho...@illumina.com > > 858-202-4582 > > > > ___ > 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 interfa

Re: [galaxy-dev] Quota

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/ > -- Ross Lazarus MBBS MPH; Associate Pro

Re: [galaxy-dev] Picard installation problem

_ > 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] Setting the output label based on input parameters?

>> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB >> wrote: >>> >>> I meant to say label="${input}" or label="${input.value}. >>> Nikhil, did you try as Shaun and others have suggested? Any available string parameter can be used in a label as far as I can tell. This is a common idiom - ask for a st

Re: [galaxy-dev] Setting the output label based on input parameters?

ok to change the output dataset name based on some logic - but if the boolean works, I'd recommend moving on :) On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi wrote: > Hi Ross, > > Yes, I did try that... but what I want is string parameter that changes > based on whether or not you

Re: [galaxy-dev] Setting the output label based on input parameters?

h > something like "s_1_1_PWDxNOD.fastqsanger.bam.gex.tab". > > Like the first of the two suggested additions I mention above, I could see > you deciding to add more possible operations in addition to basename, upper, > lower and replace. > > The concept of the ma

Re: [galaxy-dev] Error in FastQC

> 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/ > -- Ross Lazarus MBBS

Re: [galaxy-dev] accessing files_path directory in subsequent analysis steps

Nikhil, You've found an old wart - try using extra_files_path I don't remember exactly why but it's write to files_path but read from extra_files_path :0 On Fri, Sep 2, 2011 at 9:21 AM, Nikhil Joshi wrote: > Hi all, > > So I am writing XML files for an analysis pipeline.  The first step in the >

Re: [galaxy-dev] How to allow anonymous users to run workflows?

Here's one bad option for dealing with a bad requirement - at least it requires no code changes... 1. create a new user called d...@where.ever.org for your Galaxy. Do not require login in universe_wsgi.ini 2. edit welcome.html - invite visitors not wanting all the benefits of an individual registr

Re: [galaxy-dev] Command line option

> > ___ > 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://li

Re: [galaxy-dev] outputting different numbers of files based on variables?

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 lik

Re: [galaxy-dev] Setting the output label based on input parameters?

ton wrote: >> >> This is a big part of the reason we did this. >> >> I will push it out for the galaxy team to look at.  If for some reason the >> don't approve it I can share our change directly with you. >> >> Dave >> >> On Sep 1, 2011, a

Re: [galaxy-dev] Installation troubles with numpy dependency

t; Best, > Sebastian > ___ > 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: &g

Re: [galaxy-dev] Error in FastQC

ing them to run. On Sun, Sep 25, 2011 at 9:33 PM, Antonio Ribeiro wrote: > Hi Ross and Matthew, > I'm a newbie to Galaxy and got the same error while trying to process some > Illumina data... Thanks for your posting and tips! > > So, just to confirm the understanding: when insta

Re: [galaxy-dev] picard error.

:04 AM, Ross wrote: > Michael, > > Thanks for pointing these warning errors out. I think they're harmless > and can be ignored but I'll definitely take a look later today and > check in a fix. > As I recall, we had some discussion some months ago about whether to > al

Re: [galaxy-dev] applications not installed?

ind wrappers > but no apps. Where should they be located? > Thanks, > Sofia > ___ > 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] moving the galaxy-dist folder structure

ownload or update? > > joe > > ___ > 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/ > -- Ross Lazarus

Re: [galaxy-dev] fastqc in local galaxy - problem

** > Todd Oakley, Professor > Ecology Evolution and Marine Biology > University of California, Santa Barbara > Santa Barbara, CA 93106 USA > > NEWLY UPDATED LAB WEBSITE: http://labs.eemb.ucsb.edu/oakley/todd/ > ** > > __

Re: [galaxy-dev] Importing Historys in other Galaxy instances

Hi, Stefanie. I think you might want a URL pointing to an "archived history" if you want to move your history to a different Galaxy? I imported your test history into my account on main, then I used the 'export to file' option (it might not be optimally named since it really creates an importable

Re: [galaxy-dev] Importing Historys in other Galaxy instances

er.log after you start an import job that never finishes? On Tue, Oct 25, 2011 at 9:02 PM, Stefanie Ververs wrote: > Hi Ross, > > that is exactly what I tried - "Export to file" and then enter the link into > "Import from File". > But the History never appears

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

> 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/ > -- Ross Lazarus MBBS MPH; Associate Prof

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

e the file from >> extra_files_path as a history item and how would I set metadata like >> file format and db on the extra files?  Things like PDF and text work >> fine, but I'd really like to be able to have BED and WIG files in the >> history with the UCSC genome bro

Re: [galaxy-dev] Appropriate method of coalescing tool output (not workflow)

other upload, metadata may need tweaking after the upload - which is why artifacts likely needed downstream are best written as separate history items with metadata correctly set. On Tue, Nov 1, 2011 at 11:03 AM, Jesse Erdmann wrote: > On Tue, Nov 1, 2011 at 9:07 AM, Ross wrote: >> On

Re: [galaxy-dev] making data libraries from database tables

Hi James, Existing tools mostly take file paths. This has arguably useful side effects in isolating cluster node execution from the galaxy server process and persisting the computation input on a file-system - arguably more stable long term than queries on dynamic database tables - and maybe not s

Re: [galaxy-dev] microarray & NGS

Hi Ivan, > In particular the data which I'm trying to upload are > created with rexpression (incidentally, is it still > supported or novel versions are attended?), because Unfortunately, rexpression is not supported at present- the source is readily available from bitbucket but the original auth

[galaxy-dev] FastQC 0.10.0

Please ignore this message unless you maintain a local Galaxy instance and use FastQC. The most recent FastQC release 0.10.0 fixes some bugs but also completely changes the HTML layout of the report in ways that break the old wrapper. I've updated the wrapper script and tests to cope with this, so

Re: [galaxy-dev] Name your own tool's output?

I haven't. > > When porting my own tool, is there anyway to customize the name of the > output? > > Timothy > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this >

Re: [galaxy-dev] Name your own tool's output?

ever help I can... On Fri, Nov 18, 2011 at 10:50 AM, Paniagua, Eric wrote: > Hi Ross, > > That's excellent, thanks for jumping in! > > I've been charged with constructing a Galaxy tool kit for basic microarray > data analysis for my group's Galaxy instance, and I

Re: [galaxy-dev] Web links not leading to appropriate location anymore.

gt; Does anyone have an idea, a lead to explore? > > Thanks, > L-A > __**_ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy

Re: [galaxy-dev] possibly weird config requests...

have received this message in error, please notify the > sender immediately. > > -- > > > > ___ > Please keep all replies on the list by using &qu

Re: [galaxy-dev] Excel upload problems

es in Galaxy? > > Peter > > P.S. Why do you call your class XIs, surely Excel would be > clearer? > ___ > Please keep all replies on the list by using "reply all" > in your mail client.  To manage your subscr

Re: [galaxy-dev] SAM/BAM Hybrid Selection Metrics

is...maybe a file format specific for Picard formatted > BED file. > > > ___ > 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://list

Re: [galaxy-dev] Error download composite dataset from history

t; > ___ > 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] Error download composite dataset from history

Hi, L-A, 2012/1/19 Louise-Amélie Schmitt : > Hi Ross > > Thanks a million, I hg-pull'ed it solved the problem!! Please push it to > galaxy-dist? ;) Glad to hear it works - thanks for reporting back. > I ran in another little bug though, but nothing serious, you might even ha

Re: [galaxy-dev] software installs: PATH vs env.sh

;> >>>> Thanks, >>>> Andrew Warren >>>> >>>> ___ >>>> Please keep all replies on the list by using "reply all" &

Re: [galaxy-dev] tool shed offline?

ll 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/ > -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Med

[galaxy-dev] cool tool for the week

http://www.biodalliance.org/index.html embeddable - DAS native, but local server bigBed/bigWig files http://www.biodalliance.org/bin.html can be served. ___ Please keep all replies on the list by using "reply all" in your mail client. To man

Re: [galaxy-dev] Extracting the metrics files from a composite file such as Picard

> ___ > 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] Extracting the metrics files from a composite file such as Picard

e the process - of course, including the outputs in workflows when their number is not known at execution may be tricky, but at least this is a generic approach and won't require any changes to any of the tools that generate Html outputs? On Tue, Feb 21, 2012 at 8:45 AM, Anthonius deBoer wrote:

Re: [galaxy-dev] Extracting the metrics files from a composite file such as Picard

ki.g2.bx.psu.edu/Admin/Datatypes/Composite%20Datatypes > > There is a wiki on creating Composite Datatypes but not the equivalent > reading of composite datatypes, is there? > > Thon > > On Feb 20, 2012, at 07:11 PM, Ross wrote: > > Thon, I just had an idea - write a new to

Re: [galaxy-dev] strange error having to do with stderr redirection?

base\xe2\x80\x99:\n\nattach, detach, > environment, gc, load, save\n\naroma.light v1.22.0 (2011-10-31) > successfully loaded. See ?aroma.light for help.\n', 1345] > > It seems that R produces some output on stdout that I can't get rid of > yet, but it doesn't seem to a

Re: [galaxy-dev] incorrect tmp dir handling in picard AddOrReplaceReadGroups

you, > > Matt > > > > > > > -- > Matt Shirley > Ph.D Candidate - BCMB > Pevsner Lab > Johns Hopkins Medicine > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client.  To manage your subscriptions to this &

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

the same way to set other programs, such as bwa >> and bowtie, and they worked perfectly. Only samtools could >> not work. >> > I even used the full path of samtools in the wrapper >> file sam_to_bam.py, and it was not working neither. >> > >> > I am wonde

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

/data/app/lib path to the galaxy user's path so the nodes running jobs inherit those paths because of the -V switch. I hope this works! On Tue, Apr 17, 2012 at 5:10 PM, zhengqiu cai wrote: > Hi Ross, > > Thank you for your reply. > I tried it, and it was still not working. &g

Re: [galaxy-dev] Workflow import error

eg Von Kuster >> >>> >> >>> On Apr 13, 2012, at 5:22 PM, Robert Chase wrote: >> >>> >> >>>> Hello All, >> >>>> >> >>>> I'm pretty sure I found a bug in the main galaxy distribution. The >> >>&

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

ur shop and hope somebody with more experience can help out. On Wed, Apr 18, 2012 at 10:50 AM, zhengqiu cai wrote: > Hi Ross, > > Thank you for your reply. > It still did not work. > I think SGE knows the path of samtools. Here is a test case I added to > Galaxy, and it creates

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

can. On Wed, Apr 18, 2012 at 11:39 AM, zhengqiu cai wrote: > Hi Ross, > > I did not compile samtools using the --prefix. The samtools I used comes with > Galaxy AMI image, and I copied it to the same path on my EC2. How to compile > samtools using --prefix? I just typed 'mak

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

ustralia and New Zealand that are interested. I know that > there are many more Galaxy installations in that part of the world (and you > have Enis and Ross in Australia now).  Would this be a good opportunity to > set up the first (to my knowledge) regional user group?  If anyone thinks >

Re: [galaxy-dev] About Galaxy Configuration

Hi, Ciara, AFAIK new tools always require a server restart at present, but an already loaded tool can have updates to the tool XML re-read using the 'Reload a tool's configuration' option from the administrative menu if your login is listed as an administrator in the config file. Restarting Galax

Re: [galaxy-dev] Re : Error executing tool: cannot find 'database'

nit__.py", >> line 333, in execute >> data.name = fill_template( output.label, context=params ) >> File "/home/myName/work/galaxy-dist/lib/galaxy/util/template.py", line >> 9, in fill_template >> return str( Template( source=template_text, searchList=[context] ) ) >> File >> >>

Re: [galaxy-dev] wrapping qvalue in Galaxy

of solutions. > > ___ > 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://lis

Re: [galaxy-dev] I can't see or access pictures in FastQC

scriptions to this > and other Galaxy lists, please use the interface at: > >  http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ P

Re: [galaxy-dev] I can't see or access pictures in FastQC

d you haven't made any code changes, I'm going to guess that you might have a local web server configuration issue - but maybe Nate or Dan can help? On Thu, Jun 7, 2012 at 11:54 PM, Dorset, Daniel C wrote: > Hi Ross, thanks for the reply! I ran FastQC from the command line, and

Re: [galaxy-dev] I can't see or access pictures in FastQC

that's the May 9th release > > Thanks again for your help! > > Dan > -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ Please keep al

Re: [galaxy-dev] Tool Shed Workflow

hanism > for doing that, but I think you read it like I was trying to describe > a way to script the migrations of the existing official Galaxy tools > (I definitely get that you have done that). > > Thanks again for your time and detailed responses, > -John > >

Re: [galaxy-dev] Re : Composite output with self-declarated datatypes

HTML_FILE >do component="$i" > done > > But with a simple "echo $component" test, I get "HTML_FILE" as a result, > and not one of the component file. > > So is there any specified thing to do to recover the component files of a > composite f

Re: [galaxy-dev] Re : Composite output with self-declarated datatypes

? > > Furthermore, it doesn't completely work. I think my tool thinks there is > two parameters instead of only one, when seeing the two paths for my > components files. I don't know how to fix it either... > > Any ideas ? > > Thank you for your attention, > >

Re: [galaxy-dev] FastQC Tool Errors

t wondering what steps > I'm missing here to getting this to work with our Galaxy mirror, other than > just dropping the executable in place? Any suggestions? > > Thanks, > Josh > > > ___ > Please keep all replie

Re: [galaxy-dev] Configuring FastQC to run

ppreciated. > > -- > > ___ > 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 in

Re: [galaxy-dev] Multiple .CEL file import for microarray analysis

Scotland, with registration number SC005336. > > ___ > 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 inte

Re: [galaxy-dev] Problem installing local instance of Galaxy

gt; University of Nevada > ___ > 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] How to display tool instead of html WWFSMD page at start-up?

Neil, good news: the initial center panel renders static/welcome.html so easy to change. bad news: AFAIK no way to show a (dynamic) default tool form instead - others may know more.. On Mon, Jul 29, 2013 at 5:03 PM, wrote: > Hi, > > When Galaxy is started the centre column displays the

Re: [galaxy-dev] scripting galaxy installs / toolshed

Hi, Ido - untested by me but there's definitely an api under development documented at http://wiki.galaxyproject.org/ToolShedApi?highlight=%28toolshed%29%7C%28api%29 On Tue, Aug 13, 2013 at 6:45 PM, Ido Tamir wrote: > Hi, > > we would like to coordinate with another institution and their gala

Re: [galaxy-dev] edgeR Tool Shed

Hi, Richard, I see you are looking in the main toolshed. I cant speak for fcarmia's one but it doesn't do any dependency installation. The 'digital_dge' one was deprecated - I've now deleted it. The differential count models package in the statistics section of the test toolshed - http://testtools

Re: [galaxy-dev] DESeq for Galaxy

> 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 s

Re: [galaxy-dev] DESeq for Galaxy

se the interface at: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> > > ___

Re: [galaxy-dev] DESeq for Galaxy

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: >>&

Re: [galaxy-dev] DESeq for Galaxy

tool_dependency_directory]/htseq/0.5.4p3/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/INSTALLATION.log On Wed, Aug 21, 2013 at 4:38 PM, Sridhar Srinivasan < sridhar2bioi...@gmail.com> wrote: > Hi Ross, > > > i Installed through admin interface . > for pysam and freetype it showed new.

Re: [galaxy-dev] DESeq for Galaxy

navigating through the tool page in your admin interface. The htseq dependency will contain the installation log I need to see. On Wed, Aug 21, 2013 at 5:06 PM, Sridhar Srinivasan < sridhar2bioi...@gmail.com> wrote: > Hi Ross, > > I tried installing again it shows no item.. > >

Re: [galaxy-dev] error installing dependency for tool shed repository.

at was the problem - we should make it clear that you need to work on the archive contents as the action immediately following a download_by_url On Thu, Aug 22, 2013 at 11:31 AM, Curt Palm wrote: > Hi Dave, > > I made changes giving the suggestions of Ross, I got a different error and >

Re: [galaxy-dev] Manhattan/qq plots

___ > > 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 lis

Re: [galaxy-dev] Local Instance and current website are not the same

Hi Tevfik, Adam is right, but even easier assuming it goes smoothly, you should be able to install an updated version 3.3 of JJ's previous 3.2 wrapper via the Galaxy admin interface - test toolshed; SNP Analysis; snpeff_3_3_wrapper

Re: [galaxy-dev] Deseq2 wrapper question

Vipin, Search works pretty well on the toolshed - I'd recommend a search for (eg) 'star' before writing yet another rnastar toolshed wrapper and dependency package? There's an installable fubar package_rnastar and an rnastar wrapper based on Jeremy's code mentioned below - but working AFAIK - at le

Re: [galaxy-dev] Missing test results on (Test) Tool Shed

+1 I think it's been a problem with some of my repos for a while on test so possible not related to blast_datatypes - I sent this privately about 2 weeks ago: Ross Sep 13 (13 days ago) to Dave, Greg Hey Dave - any thoughts on how to fix http://testtoolshed.g2.bx.psu.edu/view/

Re: [galaxy-dev] Missing test results on (Test) Tool Shed

s > -Mir182 4.90399541739044 7.1511683493624 11.0744681203078 > 2.33130367310143e-08 8.08245865886245e-07 9.65884218207857 7189 Mir182 > -Mir181a-2 -3.04829832099813 6.94146510070354 -11.0721276255975 > 2.33760855164295e-08 8.08245865886245e-07 9.64401697815694 2817 >Mir181a-2 > -

Re: [galaxy-dev] pass regular expression

Hi, Jun. The inbuilt parameter sanitizer can be controlled - see http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set The sub-tag allows precise control and you can specify eg string.printable if you want ANY printable character in your parameter Here's an example

Re: [galaxy-dev] Error running Clustalw and HyPhy on Cloudman

Hi, Karen - how did you install clustalw? If not already done, can you please try installing the clustal repository owned by fubar from the test toolshed through your Galaxy admin interface - search/browse toolsheds? Please let me know how you go and if there's a problem I'll try to fix it for you.

Re: [galaxy-dev] Error running Clustalw and HyPhy on Cloudman

tool in your tool menu - until those manually installed ones (which may depend on clustalw2 being on the path) are removed? On Mon, Dec 2, 2013 at 8:36 AM, Karen Miga wrote: > Hi Ross, > > Thanks for your email. I have clustalw2 working now - I installed the > clustal reposit

Re: [galaxy-dev] Error running Clustalw and HyPhy on Cloudman

the env.sh file needed for the tool to find it. On Mon, Dec 2, 2013 at 9:08 AM, Karen Miga wrote: > Hi Ross, > >I did not detect any type of auto-install (?) After installing from > toolshed I did not find the binary under the /mnt/galaxy/shed_tools/ > toolshed.g2.bx.psu.edu

Re: [galaxy-dev] Error running Clustalw and HyPhy on Cloudman

y on your path. I believe the documentation explains this - if it's not clear please suggest some revisions ? On Mon, Dec 2, 2013 at 9:18 AM, Karen Miga wrote: > Hi Ross, > > That is listed as "tool_dependency_dir = /mnt/galaxy/tools" in my > universe_wsgi.ini file,

Re: [galaxy-dev] Error running Clustalw and HyPhy on Cloudman

; Karen > > > On Sun, Dec 1, 2013 at 2:23 PM, Ross wrote: > >> Just to confirm, you used automated installation via the admin menu -> >> search and browse toolsheds -> test toolshed -> etc ? >> If you installed manually by downloading and unpacking t

Re: [galaxy-dev] SRA datatype

Hi, Todd, The search bar at https://wiki.galaxyproject.org/ is always a good place to find stuff like https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes?highlight=%28converters%29 I hope this gets you started On Sat, Feb 8, 2014 at 12:22 PM, Todd Oakley wrote: > Hello, >

Re: [galaxy-dev] space in text tool results in two arguments

Hi Ketan. Please try quotation marks to enclose any parameter containing spaces in the tool command template - eg something like: python myscript.py "$text_with_spaces" $param2 $param3 Please confirm that this solves the problem? On Tue, Feb 18, 2014 at 12:47 PM, Ketan Maheshwari < ketancma

Re: [galaxy-dev] space in text tool results in two arguments

Hi Ketan - great news - all the best with your project... On Tue, Feb 18, 2014 at 3:58 PM, Ketan Maheshwari wrote: > Ross, > > That's correct. It seems I tested on a cached copy of tool. Works now! > > Thanks, > Ketan > > > On Mon, Feb 17, 2014 at 10:55 PM, R

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

if a tool failed we all really benefit from seeing as much as we can - as securely as we can. Can we safely expose them somewhere protected? On Thu, Feb 20, 2014 at 8:59 PM, Peter Cock wrote: > , > > On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster wrote: > > Hi Peter, > > > > On Wed, Feb 19, 20

Re: [galaxy-dev] . Output file to history (Sebastian Luna Valero)

Hi, Jun and Sebastian, This is not trivial, but it is already being done with some tools using the method described at https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Single_history_output_Html_file_with_links_to_any_number_of_output_files_and_images if that can solve your pro

Re: [galaxy-dev] Functional Tests and ftype

Hi, Saket - 436 tests in 19.153 seconds means something odd (or fast) with your setup? What errors do you see? Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4J On Thu, Apr 17, 2014 at 10:43 PM, S

Re: [galaxy-dev] uploading data libraries options

Hi, Mark, Perhaps you need to adjusted universe_wsgi.ini where it says: # Add an option to the admin library upload tool allowing admins to paste # filesystem paths to files and directories in a box, and these paths will be # added to a library. Set to True to enable. Please note the security # i

Re: [galaxy-dev] Galaxy Error Message

FWIW: looks like a trivial xml syntax error is in this line: interpreter="Rscript"> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $pathway.id $species $out.suffix $output .*..* There seem to be one too many ">" - the first one is pr

Re: [galaxy-dev] ClustalW jobs aren't working

Malcolm, It looks like you have downloaded the wrapper and put it in your local tools folder. We strongly recommend that you remove the tool_conf.xml entry and get the local galaxy administrator to install the devteam clustalw repository from the main toolshed. That should solve your problem - plea

Re: [galaxy-dev] ClustalW jobs aren't working

if it persists on recent Galaxy code we'll need to do some deeper investigation. On Fri, Jun 6, 2014 at 11:32 PM, Malcolm Tobias wrote: > > > Ross, > > > > Thanks for the reply! Unfortunately I am the local Galaxy admin ;-) > > > > I had tried installing th

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