Re: [galaxy-dev] Settings multiple Genome Indices

2014-07-28 Thread Jeremy Goecks
’)} Finally, I like your indexing syntax, and it would be great to use something like that in place of the explicit method call above. Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Jul 27, 2014, at 10:44 AM, Geert Vandeweyer geert.vandewey

Re: [galaxy-dev] Trackster : Error visualising VCF

2014-04-21 Thread Jeremy Goecks
for this VCF: sed -E 's/^[0-9XY]+/chr/‘ input.vcf | sed -E 's/^MT/chrM/' You may need to massage it depending on your platform and sed version. Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Apr 20, 2014, at 11:27 AM, Saket Choudhary sake

Re: [galaxy-dev] Trackster shared Visualization in an iframe

2014-04-17 Thread Jeremy Goecks
This is a good idea, and I’ve implemented it in this -central changeset: https://bitbucket.org/galaxy/galaxy-central/commits/c055181847a46dc3199458d899d28d559ae43c38 If you’re working with galaxy-dist, you can pull this one changeset and use it until the next release. Let me know if you have

Re: [galaxy-dev] Problem upgrading bx-python to fix trackster error.

2014-04-16 Thread Jeremy Goecks
Hi Will, This should be fixed as of this commit: https://bitbucket.org/galaxy/galaxy-central/commits/3a154b52090316dee61f42993eaa5a1fa40116d3 Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Apr 9, 2014, at 10:03 PM, William Holtz who

Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster

2014-04-16 Thread Jeremy Goecks
Hi Raj, Thanks for sharing your datasets. This issue should be fixed as of this commit in -central: https://bitbucket.org/galaxy/galaxy-central/commits/3a154b52090316dee61f42993eaa5a1fa40116d3 Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University

Re: [galaxy-dev] [galaxy-user] Trackster error on dbkeys

2014-04-10 Thread Jeremy Goecks
or lines are allowed. If you check the len file and don’t spot an issue, please send to it to me and I’ll take a look. Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Apr 10, 2014, at 2:30 AM, Aarthi Mohan aarthimoha...@gmail.com wrote

Re: [galaxy-dev] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7

2014-03-29 Thread Jeremy Goecks
I cloned directly from galaxy-dist: % hg clone https://bitbucket.org/galaxy/galaxy-dist/ which gives you the latest release, and it is 2014.02.10--2–29ce93a13ac7 Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 29, 2014, at 3:02 AM

Re: [galaxy-dev] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7

2014-03-28 Thread Jeremy Goecks
. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 27, 2014, at 4:28 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi Jeremy, I reverted the files that I have changed, and also cleaned the cache once again. The error messages are the same: Failed

Re: [galaxy-dev] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7

2014-03-26 Thread Jeremy Goecks
This sounds like a cache issue. Both of these scripts have been removed from the distribution, so they should be absent from the distribution. Can you try clearing your cache and see if that fixes the issue? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George

Re: [galaxy-dev] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7

2014-03-26 Thread Jeremy Goecks
The next step then is to revert all the changes that you pulled from -central and report back the errors you’re seeing. Manually pulling selected change sets can be problematic if you don’t get all the dependencies. Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George

Re: [galaxy-dev] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7

2014-03-25 Thread Jeremy Goecks
and provide any errors that you see? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 24, 2014, at 11:38 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi all, We have recently updated our local Galaxy installation to vrelease_2014.02.10--2

Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster

2014-03-05 Thread Jeremy Goecks
; if it fails on our public server, share the datasets with me and I'll take a look. Thanks, J. -- Jeremy Goecks Assistant Professor, Computational Biology Institute George Washington University On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam ra...@uga.edu wrote: Hello, I am trying

Re: [galaxy-dev] HTML form of select parameter

2014-01-27 Thread Jeremy Goecks
On Jan 27, 2014, at 9:57 AM, John Chilton chil...@msi.umn.edu wrote: The swap over happens when the number of items gets sufficiently large and a jQuery-based widget called select2 replaces all select boxes in Galaxy - unless explicitly disabled. I understand the desire to disable this. I am

Re: [galaxy-dev] Tophat2 Output file error

2014-01-15 Thread Jeremy Goecks
On which Galaxy server are you running your analyses? Using a current Galaxy instance and Tophat v2.0.10, I wasn't able to reproduce the issue. Thanks, J. -- Jeremy Goecks Assistant Professor, Computational Biology Institute George Washington University On Jan 13, 2014, at 11:28 AM, Bankers

Re: [galaxy-dev] faToTwoBit: not found / trackster

2014-01-06 Thread Jeremy Goecks
Ok, then it's very likely a PATH issue. There's no magic needed here - faToTwoBit simply needs to be on your path. It seems you've tried debugging this already; one suggestion is to provide the full path to the executable and see if that works. -- Jeremy Goecks Assistant Professor

Re: [galaxy-dev] faToTwoBit: not found / trackster

2014-01-06 Thread Jeremy Goecks
Ok, then it's very likely a PATH issue. There's no magic needed here - faToTwoBit simply needs to be on your path. It seems you've tried debugging this already; one suggestion is to provide the full path to the executable and see if that works. -- Jeremy Goecks Assistant Professor

Re: [galaxy-dev] faToTwoBit: not found / trackster

2014-01-04 Thread Jeremy Goecks
Can you run the faToTwoBit tool from the command line? It can be difficult to find the right executable for UCSC tools sometimes; if you have the wrong executable (e.g. 32 bit instead of 64 bit), you'll see the misleading 'not found' error. Best, J. On Jan 3, 2014, at 11:35 AM, Jasper Jan

Re: [galaxy-dev] faToTwoBit: not found / trackster

2014-01-04 Thread Jeremy Goecks
Can you run the faToTwoBit tool from the command line? It can be difficult to find the right executable for UCSC tools sometimes; if you have the wrong executable (e.g. 32 bit instead of 64 bit), you'll see the misleading 'not found' error. -- Jeremy Goecks Assistant Professor, Computational

Re: [galaxy-dev] problems with exporting or importing data from file

2013-12-18 Thread Jeremy Goecks
However, nothing is visible in my histories list. What could be wrong? I also don’t see any error messages in the log above. Thanks and regards, Pieter. From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Jeremy Goecks Sent

Re: [galaxy-dev] trackster error for viewing rat data (rn5)

2013-11-22 Thread Jeremy Goecks
this piece of useful information, i might had spent days and days on this : ) Best regards, Shu-Yi On Nov 22, 2013, at 2:40 AM, Jeremy Goecks wrote: This appears to be an issue with the dataset that you're trying to view, not the build or visualization. It appears that the (bigwig? bigbed

Re: [galaxy-dev] reasonable linux box specs

2013-11-16 Thread Jeremy Goecks
Without details about your incoming data rate and size, it's very difficult to answer this question. I suggest taking some of your data, running it on our public server (usegalaxy.org), and seeing how long it takes. RNA-seq tools (Tophat, Cufflinks, etc.) use 4 cores for a job, so you can

Re: [galaxy-dev] reasonable linux box specs

2013-11-15 Thread Jeremy Goecks
Without details about your incoming data rate and size, it's very difficult to answer this question. I suggest taking some of your data, running it on our public server (usegalaxy.org), and seeing how long it takes. RNA-seq tools (Tophat, Cufflinks, etc.) use 4 cores for a job, so you can

Re: [galaxy-dev] Empty tool panel

2013-11-15 Thread Jeremy Goecks
Do you see any errors in the JavaScript console? Does this only happen on particular Web browsers? J. On Nov 15, 2013, at 10:15 AM, Yec'han Laizet ylai...@pierroton.inra.fr wrote: Hi, In the current version of galaxy stable branch (5c789ab4144a), the tool panel is empty when installed

Re: [galaxy-dev] trackster: missing graphs for large number of contigs

2013-10-28 Thread Jeremy Goecks
in the console. Thanks, Thomas Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Gesendet: Dienstag, 22. Oktober 2013 15:55 An: Berner, Thomas Cc: galaxy-dev@lists.bx.psu.edu Betreff: Re: [galaxy-dev] trackster: missing graphs for large number of contigs A couple questions

Re: [galaxy-dev] Why are Custom Builds disabled when

2013-10-28 Thread Jeremy Goecks
Why are Custom Builds only enabled if you're *not* using remote_user ? Is this because they're related to user preferences (as per the code in lib/galaxy/webapps/galaxy/controllers/user.py)? This may be an artifact of a time when user preferences were immutable. Do Custom Builds and

Re: [galaxy-dev] trackster: missing graphs for large number of contigs

2013-10-22 Thread Jeremy Goecks
A couple questions: (a) are you using a custom build? If so, does the build show the correct number of chromosomes? (b) do you see any errors in the JavaScript console when trying to view the BAM file? Thanks, J. On Oct 21, 2013, at 11:05 AM, Berner, Thomas thomas.ber...@jki.bund.de wrote:

Re: [galaxy-dev] Share workflows for all users

2013-10-21 Thread Jeremy Goecks
For your workflow, try going to 'Share or Publish' option -- and share via URL (and publish it if you want). The workflow can then be shared with a large number of people using the URL. Best, J. On Oct 21, 2013, at 4:07 AM, Anatoliy Pandorin pandorin...@gmail.com wrote: For a long time I

Re: [galaxy-dev] page editor problem when saving Chinese

2013-10-18 Thread Jeremy Goecks
This issue was fixed in this changeset: https://bitbucket.org/galaxy/galaxy-central/commits/8c663e656f64a60dac55979841947e78ce23a473 If you update your Galaxy to the revision on galaxy-dist this problem should go away. Best, J. On Oct 18, 2013, at 1:10 PM, lardo la...@qq.com wrote: I run a

Re: [galaxy-dev] Access to history_id from tool config XML

2013-09-26 Thread Jeremy Goecks
I'm still not fully understanding your usage scenario. A simple example is the creation of a full history based log file. I imagine that this would be an ideal use of the history API. Rather than having tools log history, write a script that uses the API to generate a history log. My more

Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version

2013-09-25 Thread Jeremy Goecks
to get the 0.0.6 version., Any idea what I’ve missed? Regards, Curtis From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Thursday, September 19, 2013 3:17 PM To: Curtis Hendrickson (Campus) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cuffdiff wrapper

Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version

2013-09-25 Thread Jeremy Goecks
From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Wednesday, September 25, 2013 8:43 AM To: Curtis Hendrickson (Campus) Cc: galaxy-dev@lists.bx.psu.edu; Shantanu Pavgi (Campus) Subject: Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version The problem

Re: [galaxy-dev] Visualisation of VCF files in trackster

2013-09-25 Thread Jeremy Goecks
Thanks for reporting this issue and workaround Ulf. I've committed a fix that addresses this issue by only includeing the -split option for BED/GFF/GTF datasets and not VCF: https://bitbucket.org/galaxy/galaxy-central/commits/b8d8f81bed872e58b4691643de8a08fa41662e71 Best, J. On Sep 12, 2013,

Re: [galaxy-dev] Access to history_id from tool config XML

2013-09-23 Thread Jeremy Goecks
At line ~694: incoming['__user_name__'] = user_name + if job.history and job.history.id: + incoming['__history_id__'] = job.history.id + else: + incoming['__history_id__'] = 'unknown' I have tested this change and it appears to give me exactly what I

Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version

2013-09-19 Thread Jeremy Goecks
I know the general versioning problem is address through the tool-shed mechanism, but for the remaining core wrappers, can maintainersplease update wrapper version numbers when making changes? Not bumping wrapper versions is an oversight, not deliberate. For this wrapper set, how would

Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version

2013-09-19 Thread Jeremy Goecks
We can hack the old wrapper back in, using a hard-coded path to the old cuffdiff. You could also use Managed Tool Dependencies for multiple versions of cuffdiff: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies Shantanu suggests it might be a better world if we create a

Re: [galaxy-dev] CuffDiff read group tracking

2013-09-16 Thread Jeremy Goecks
: Hey Galaxy, I am trying to use CuffDIff with replicate analysis on a local instance. I saw that Jeremy Goecks had a solution to this problem: http://user.list.galaxyproject.org/Cuffdiff-changes-tt4655893.html#a4655901. Could I see/use this source code please? I can't really wait until

Re: [galaxy-dev] Geek question re HTTP POST and Galaxy

2013-09-16 Thread Jeremy Goecks
hi Jeremy, in the histories controller, I could find no example to nicely obtain the PUT and POST content payload. Am I missing it? So I think a bad answer to my question is the following code. But I really don't like my _get_payload() hack reaching into the trans.environ object. Is

Re: [galaxy-dev] Conditional and validator: refresh_on_change without validation

2013-09-14 Thread Jeremy Goecks
You're not missing anything; using validators is the right way for checking parameter values. However, the page refreshes + validation errors is certainly less than ideal for usability. We're in the process of transitioning tool forms to a JavaScript-based framework so that full page refreshes

Re: [galaxy-dev] Geek question re HTTP POST and Galaxy

2013-09-14 Thread Jeremy Goecks
Take a look at the histories controller (histories.py) for an example + documentation on how Galaxy realizes a RESTful interface. In short, you'll want to implement different methods for create, read, update, and delete. Kwds are miscellaneous parameters included in a request that are not

Re: [galaxy-dev] Scaling and hardware requirements

2013-09-12 Thread Jeremy Goecks
This isn't an easy question to answer. Here's why: *there is significant variation in mammalian genome size; of course, larger genomes require more resources, but the relationship is difficult to quantify; *assembly can take anywhere from a day to a week depending on software and resource

Re: [galaxy-dev] Visualisation of VCF files in trackster

2013-09-11 Thread Jeremy Goecks
My attempts to visualise a vcf file in trackster fail. I can visualise the corresponding SAM/BAM files fine. I can visualise the same file on Galaxy main too, but not in my local install. To be clear, you can visualize the VCF dataaset on main but not locally? Can you visualize SAM/BAM

Re: [galaxy-dev] Deseq2 wrapper question

2013-09-11 Thread Jeremy Goecks
STAR aligner I have a partial STAR wrapper that may be useful: https://bitbucket.org/jgoecks/jeremys-code/src/d7096c132657420f08b540c6954b947f648aac80/galaxy/tool-wrappers/star.xml?at=default Whether you use this code or not, I do have one request: please put the output in BAM rather than

Re: [galaxy-dev] Circumvent Show all button

2013-09-10 Thread Jeremy Goecks
There is currently no simple way to circumvent this behavior. If you want to modify the code, take a look at display_data() in data.py -- you'll want to bump up the max_peek_size (line 351 in -central) above 10 MB for HTML datasets. Good luck, J. On Sep 9, 2013, at 6:16 AM, Gromobir wrote:

Re: [galaxy-dev] options from_dataset evaluation in workflow

2013-09-07 Thread Jeremy Goecks
Dear all, in one of my tools I'm populating a list of possible choices from a file in the history using the options from_dataset tag. Now using the tool as part of a workflow, the choices are not calculated at the setup stage, but I have to enter free-text and Galaxy seems to evaluate

Re: [galaxy-dev] API question: is it possible to start exporting histories

2013-09-06 Thread Jeremy Goecks
Is it currently possible to export histories via the API? Not possible yet but is definitely something we'd like to implement and/or see from a community contribution. Best, J. ___ Please keep all replies on the list by using reply all in

Re: [galaxy-dev] Trackster: alignment is not showing up as 'squish'

2013-09-05 Thread Jeremy Goecks
I suspect there is an issue with Trackster when changing from one mode to another. Can you confirm that by saving and refreshing the visualization, you can view the dataset in different modes? Thanks, J. On Sep 5, 2013, at 4:06 AM, Joachim Jacob | VIB | wrote: Update: the 'dense' option does

Re: [galaxy-dev] [galaxy-user] Questions regarding Galaxy Tool XML File

2013-09-03 Thread Jeremy Goecks
Question: How save is the optional attribute ? I mean how consequent are you in this matter when the tool definition xml is to be created. It's not clear to me what you're asking. That said, it's important to distinguish between Galaxy tool wrappers and their corresponding tools. Either

Re: [galaxy-dev] How to configure and set up the Circos on my local Galaxy?

2013-09-03 Thread Jeremy Goecks
Please take a look at this page for setting up visualizations: http://wiki.galaxyproject.org/Visualization%20Setup Let us know if you have any questions. Best, J. On Sep 1, 2013, at 9:37 PM, shenwiyn wrote: Hi , I found that the visualization of Circos works greatly in Galaxy main,but

Re: [galaxy-dev] Select multiple and conditional

2013-08-27 Thread Jeremy Goecks
As you discovered, this isn't possible yet. You'll need to break up your parameters into multiple conditions, so Yes/No for Blast and Yes/No for Fasta. Best, J. On Aug 26, 2013, at 6:33 AM, Kahlke Tim wrote: Hei, Is it possible to use a select multiple=True for a conditional? I'm trying

Re: [galaxy-dev] RuntimeError: maximum recursion depth exceeded while calling a Python object

2013-08-27 Thread Jeremy Goecks
There are sporadic reports of this issue, but I haven't been able to reproduce it. My best guess is that it's due to trying to use the custom build before Galaxy has finished creating it. To ensure that the custom build is ready for use, make sure to wait for Galaxy to show the number of

Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?

2013-08-24 Thread Jeremy Goecks
It appears you are missing some updates. This issue was fixed in this changeset 9992: -- changeset: 9992:7105c53139d4 branch: stable parent: 9990:f35c0441e374 user:jeremy goecks jeremy.goe...@emory.edu date:Tue Jun 11 17:34:26 2013 -0400 files: lib/galaxy/tools

Re: [galaxy-dev] enable to edit pages

2013-08-01 Thread Jeremy Goecks
This bug has been fixed in our code repository and will be included in our next release, which is due out in a couple weeks. Best, J. On Aug 1, 2013, at 1:25 AM, Philipe Moncuquet wrote: Hi guys, Since the last update of Galaxy. We are enable to edit pages on our local instance. Pages

Re: [galaxy-dev] How to display tool instead of html WWFSMD page at start-up?

2013-07-30 Thread Jeremy Goecks
: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Tuesday, 30 July 2013 12:37 PM To: Burdett, Neil (ICT Centre, Herston - RBWH) Cc: ross.laza...@gmail.com; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] How to display tool instead of html WWFSMD page at start-up? You'll need

Re: [galaxy-dev] How to display tool instead of html WWFSMD page at start-up?

2013-07-29 Thread Jeremy Goecks
, in fix_call val = callable(*args, **kw) TypeError: make_prefix_middleware() got an unexpected keyword argument 'welcome_url' I can’t find anywhere in the code that has the test string “welcome_html” Any ideas? Thanks Neil From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent

Re: [galaxy-dev] HTML output with external Javascript

2013-07-25 Thread Jeremy Goecks
The file that Gift is producing is already an html file and there's already an html datatype in Galaxy by default. The output file in question just invokes remote javascript libraries inside script tags, and this seems to be tripping up Galaxy's data viewer. Setting up relative paths to

Re: [galaxy-dev] Bowtie2 error: Creates a 62 kb file.

2013-07-24 Thread Jeremy Goecks
It would be very useful to know what's in the 62kb file -- is it a BAM file or a long error message? Also, the Bowtie2 wrapper has been updated in -central, so you may want to check that out as well. J. On Jul 24, 2013, at 5:07 PM, Maddhi, Srinivas wrote: [Copying the list].

Re: [galaxy-dev] tool input is folder rather than file

2013-07-24 Thread Jeremy Goecks
You'll want to use composite datatypes: http://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes On Jul 24, 2013, at 3:08 AM, Pankaj Narang wrote: Dear Developers, I want to design a tool whose input is folder containing files and sub-folders. I was wandering which value

Re: [galaxy-dev] FastQC files are not being recognized by

2013-07-19 Thread Jeremy Goecks
Fastq datasets can have many different encodings for quality scores. See here for details: http://en.wikipedia.org/wiki/FASTQ_format Many tools in Galaxy require that fastq datasets be in fastqsanger format and designated as such in its datatype. Because your data appears to be in

Re: [galaxy-dev] tool inheritance

2013-07-18 Thread Jeremy Goecks
What you envision probably isn't possible yet. Two ideas for extending Galaxy: (1) use the show structure functionality from the history menu to generate a summary page or (2) create a Pages API and implement a function to create and save a new page that describes the structure. Best, J.

Re: [galaxy-dev] cummerBund installation

2013-07-12 Thread Jeremy Goecks
The toolshed has a wrapper for cummerbund: http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund On Jul 12, 2013, at 12:03 AM, sridhar srinivasan wrote: Dear Developers, Could you please tell me the possibilities of using the R package cummeRband for visualization of RNA-seq data in

Re: [galaxy-dev] Trackster and bedtools error

2013-07-12 Thread Jeremy Goecks
bedtools genomecov -bg -split -i stdin -g /usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len However this crashes. After looking in my computer, I find that bedtools do not contain the file genomecov. Is this an erroneous assumption of mine or have I installed something

Re: [galaxy-dev] Exit_code not working anymore

2013-07-12 Thread Jeremy Goecks
This is a known issue that we have plans to fix. You can follow our progress here: https://trello.com/c/JfB2w1Br Best, J. On Jul 12, 2013, at 6:09 AM, Mathieu Bahin wrote: Hi all, We have a Galaxy instance that we are regularly keeping up to date following the Galaxy main, so we have

Re: [galaxy-dev] Short-term access to a galaxy server for teaching

2013-07-11 Thread Jeremy Goecks
Here's a cloud image that the Galaxy team often uses for workshops: http://wiki.galaxyproject.org/CloudWorkshop Good luck, J. On Jul 11, 2013, at 1:28 PM, Maddhi, Srinivas wrote: Hi Max, An alternative approach, in case that becomes necessary, would be to set up your own temporary

Re: [galaxy-dev] queue system

2013-07-10 Thread Jeremy Goecks
You have two options: (1) set the number of workers in the LocalJobRunner; (2) Galaxy can use many different computing clusters, all of which have queuing systems that you can control. See this page for more details on both options:

Re: [galaxy-dev] Trackster and bedtools error

2013-07-09 Thread Jeremy Goecks
You'll need to make sure that bedtools is in your Galaxy user's path. Best, J. On Jul 9, 2013, at 6:40 PM, Perez, Ricardo wrote: Dear all, As I was trying to do visualize my data set in trackster, I get the following error: /bin/sh: 1: bedtools: not found sort: fflush failed: standard

Re: [galaxy-dev] Question about bowtie2_indeces.loc

2013-07-07 Thread Jeremy Goecks
Dbkey specifies the base assembly; unique build ID species the particular assembly. This is most often used for human assemblies: dbkey is hg19 and build ID might specify some combinations of autosomes, sex chromosomes, and mitichondrial DNA. J. On Jul 6, 2013, at 6:16 PM, Perez, Ricardo

Re: [galaxy-dev] samtools BAM to SAM tmp directory

2013-07-03 Thread Jeremy Goecks
That's certainly neater. There are many more wrapper that do the same - using mkdtemp() without a dir argument. Is there any plan to perform the same changes on these (bam-to-sam, etc...)? I made the same change for the BAM to SAM wrapper so that it create temp files in the job working

Re: [galaxy-dev] samtools BAM to SAM tmp directory

2013-07-02 Thread Jeremy Goecks
In the spirit of this solution, I've implemented something similar in -central changeset: https://bitbucket.org/galaxy/galaxy-central/commits/c7a07f350887fe3b4e822ba6b26b63ac3ac14bdf The tool now creates temporary files in its working directory, which can be configured via the

Re: [galaxy-dev] Insert link in page editor

2013-07-01 Thread Jeremy Goecks
Can anyone comment on this? Why insert a weird non-user friendly WYM stamp guid? Just unfinished functionality. It's fixed in -central changeset 2cabbf368763 and will be available on our public server in a couple weeks. Best, J.

Re: [galaxy-dev] Upload files to data library

2013-07-01 Thread Jeremy Goecks
To follow up on that, I thought it would be useful to have that mentioned in the wiki. I did some modifications to indicate the necessary changes to be done to universe_wgi.ini file (http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles). I hope that is OK. Besides,

Re: [galaxy-dev] Upload files to data library

2013-06-28 Thread Jeremy Goecks
You'll need to update the settings in your universe_wgi.ini file (and restart Galaxy) to get these options to show up; specifically, take a look at 'library_import_dir' and 'allow_library_path_paste' Best, J. On Jun 28, 2013, at 2:22 AM, Lionel Guy wrote: Hi! I'm trying to upload multiple

Re: [galaxy-dev] Bowtie2 Specifying -k value (Alignment Search)

2013-06-26 Thread Jeremy Goecks
I was looking at galaxy/dist/tools/sr_mapping/bowtie2_wrapper.* and it does not seem to challenging to add another field where a user could specify some integer value that we simply pass to the the command tag in the xml file. Would this be the correct way to go about this? Yes, this is

Re: [galaxy-dev] Path to the bedtools for getting trackster working properly

2013-06-26 Thread Jeremy Goecks
To have Trackster visualization working properly in Galaxy, one needs bedtools. Yet in our instance (running under Ubuntu OS), installing bedtools in the galaxy home directory and setting the environmental variable PATH in the .profile file so that it includes the path to ~/bin/bedtools

Re: [galaxy-dev] validation for tools

2013-06-25 Thread Jeremy Goecks
dwgsim (and dwgsimeval) may be useful to you: http://toolshed.g2.bx.psu.edu/view/nilshomer/dwgsim http://toolshed.g2.bx.psu.edu/view/nilshomer/dwgsim_eval Good luck, J. On Jun 24, 2013, at 11:47 PM, מירב . wrote: Hi, I want to do some checks on tools I'm using(in this case I'm checking

Re: [galaxy-dev] Error in using Trackster: datatypes_conf.xml

2013-06-25 Thread Jeremy Goecks
A converted for this file is not installed. Please heck your datatypes_conf.xml file. How exactly do I find out which converted files I am missing? This information isn't easy to find yet, so I've created a card for it: https://trello.com/c/E3ReiSVU If you haven't modified your

Re: [galaxy-dev] galaxy cuffdiff running too long

2013-06-24 Thread Jeremy Goecks
Error running cuffdiff. [12:48:21] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [12:48:33] Inspecting maps and determining fragment length distributions. terminate called after throwing an instance of

Re: [galaxy-dev] API updating meta data for a history

2013-06-20 Thread Jeremy Goecks
Take a look at the item_tags API controller; you can manage (add/delete/show) history, dataset, and workflow tags using it. There's not much documentation for it yet, but it should be pretty straight-forward. Let us know if you have questions. Best, J. On Jun 20, 2013, at 9:59 AM, Philip

Re: [galaxy-dev] simplest way to connect RNAseq tools for a local Galaxy instance

2013-06-20 Thread Jeremy Goecks
Here's some specific information about what the PATH variable is for UNIX systems and how to set it: http://kb.iu.edu/data/acar.html Many folks do the following so that you only need to add a single directory to your path: (a) install all tools in one directory; (b) create a bin directory in

Re: [galaxy-dev] transferring Trapnell et al programs into a one user instance of Galaxy

2013-06-16 Thread Jeremy Goecks
Elwood, It's not clear what steps you're having problems with, so it's difficult to offer help. Here's the outline that I use to RNA-seq running with Galaxy: *download Samtools, Bowtie2, Tophat2, and the Cufflinks tool suite and add them to my galaxy user's path; *download the iGenomes data

Re: [galaxy-dev] problem integrating new jar file

2013-06-16 Thread Jeremy Goecks
You'll need to (a) add an output file to your tool configuration ( see http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coutputs.3E_tag_set ) and (b) write your output to the file. See other tool wrappers (e.g. /tools/filters/cutWrapper.xml) for an example. Good luck, J. On Jun

Re: [galaxy-dev] Download histories

2013-06-14 Thread Jeremy Goecks
You'll need to wait until the history is ready for download -- i.e., Galaxy provides a .gz file rather than a Webpage at that URL -- before using wget. Galaxy returns a webpage (text/html) while preparing the history for download; this is likely what you are downloading now. Good luck, J.

Re: [galaxy-dev] Recently Used Histories

2013-06-12 Thread Jeremy Goecks
My use case involves working with a lot of histories, and I need to jump back and forth between them fairly frequently. However, it's a bit inconvenient to have to click on the Options button on the rightmost pane, Saved Histories in the drop-down menu, and select my history on the main pane.

Re: [galaxy-dev] cuffdiff wrapper not synchronized with cuffdiff version

2013-06-12 Thread Jeremy Goecks
Hello, After the latest update of Galaxy I saw that the cuffdiff wrapper is for version 2.0. I updated the $PATH to cuffdiff v. 2.0.2 but when I run cuffdiff in Galaxy I get the following error: Error running cuffdiff. cuffdiff: /lib64/libz.so.1: no version information available

Re: [galaxy-dev] Trackster set display mode - Output looks all the same

2013-06-11 Thread Jeremy Goecks
Hi Linda, 1- Should the "Set display mode" give out different output?Not yet.VCF visualization is new to Galaxy, and mode switching isn't implemented yet. (It will be implemented in the next release.)What you're seeing is the display of individual variants; of course, trying to view so many

Re: [galaxy-dev] problems with exporting or importing data

2013-06-11 Thread Jeremy Goecks
Anna, Try following these steps: (1) Make your history accessible (Share or Publish -- Make History Accessible by Link). (2) Export your history again; make sure to wait until you can use the URL to download a .gz file of your history. (3) Try importing it via URL to the Huttenhower Lab

Re: [galaxy-dev] Trackster error: not able to find the chrom len file

2013-06-11 Thread Jeremy Goecks
Trackster displays an error after opening a saved view: *** Error: The requested genome file (/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not be opened. Exiting! sort: write failed: standard output: Broken pipe sort: write error Couldn't open

Re: [galaxy-dev] Can I use javascript in the xml to select a date on a calender?

2013-06-07 Thread Jeremy Goecks
I want to select a date from a calender in my tool, but I think that it's not possible in the xml. Correct, date inputs are not currently implemented in Galaxy parameters. Is this possible? With javascript? Or what? It's possible if you want to extend Galaxy a bit. I suggest (a) adding a

Re: [galaxy-dev] mapping Summary from Bowtie

2013-06-04 Thread Jeremy Goecks
how to get the mapping summary from bowtie2 using galaxy interface.. This isn't possible right now, but I've filed a Trello card that you can follow to watch progress on this enhancement: https://trello.com/c/yFeXvhUg Of course, a patch/contribution addressing this issue would be fantastic.

Re: [galaxy-dev] import Workflow from public Galaxy to local instance

2013-05-30 Thread Jeremy Goecks
I tracked down this issue to a bug in the workflow export code, and I've fixed it. The fix will appear on our public server early next week; please let us know if you're still seeing this error late next week. Best, J. On May 23, 2013, at 9:50 AM, Andreas Kuntzagk wrote: For the first of

Re: [galaxy-dev] cufflinks in the main galaxy instance is not able to produce compatible FPKM score

2013-05-29 Thread Jeremy Goecks
These are options we'd like to add to Cufflinks, and I've created a Trello card for this enhancement: https://trello.com/c/U7nceKdj I want to add that community contributions via patch or pull request are highly encouraged and are likely to be quicker than waiting for the core team to get to

Re: [galaxy-dev] organizing datasets in the history

2013-05-29 Thread Jeremy Goecks
When a user creates an account, s/he can create/copy/delete histories and copy datasets from history to history to organize data. Each history, then, is a like a library folder. Best, J. On May 29, 2013, at 11:02 AM, 吳正華 wrote: Hi, galaxy community: I’ve set up a local galaxy for our

Re: [galaxy-dev] Displaying genomic sequences in Trackster

2013-05-24 Thread Jeremy Goecks
Hello! I am trying to enable Trackster on our local galaxy to visualize the mapping results. But, so far, it is not working. Is the twobit.loc file necessary for using Trackster? or is it just optional? Best regards, Menorca Twobit files, configured via twobit.loc, are optional. Here is

Re: [galaxy-dev] Samtools and idxstats

2013-05-22 Thread Jeremy Goecks
Galaxy stores a BAI for each BAM internally; you can access it in a tool wrapper like this (assuming the name of your input dataset is 'input_bam': ${input_bam.metadata.bam_index} Once you have the file path, you can set up a symbolic link to it and the tool should work fine. Good luck, J.

Re: [galaxy-dev] Workflow annotations

2013-05-14 Thread Jeremy Goecks
On the other hand, if a workflow is imported from a file on disk or from a URL, tool level annotations are available while workflow level annotations are not. This has been fixed in this changeset: https://bitbucket.org/galaxy/galaxy-central/commits/8882e45504a3/ Thanks for reporting this

Re: [galaxy-dev] Embedding a help text in a Workflow?

2013-05-10 Thread Jeremy Goecks
Do you think we could add a new 'rich text' field for a workflow free text help / readme file? Annotations will support HTML, and it's always been the long-term plan that they will include HTML. What's missing is a nice editor for creating HTML annotations. J.

Re: [galaxy-dev] How to transfer or upload datasets to Galaxy server automatically?

2013-05-09 Thread Jeremy Goecks
You can probably use the API for what you want to do, though your users will need to have an API key to make everything work smoothly. Documentation for the API is here: https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html An alternative approach would be to

Re: [galaxy-dev] Published Workflows missing from All Workflows

2013-05-06 Thread Jeremy Goecks
i.e. Published Workflows are hidden or separated away from the others. This appears to be a design choice (like shared datasets they must be imported before use), but if so this could be clarified as follows: This was a very old design choice that will be revisited in the (hopefully near)

Re: [galaxy-dev] List of genomes

2013-05-06 Thread Jeremy Goecks
You can add genomes in this file: $GALAXYROOT/tool-data/shared/ucsc/builds.txt Note that without related files (e.g. genome sequence, indices for mapping), the build information isn't very useful. However, with an entry in this file, you can link it to other resources when they become

Re: [galaxy-dev] traceback - local error?

2013-04-24 Thread Jeremy Goecks
File /mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py, line 1170, in _get_dataset return f, BigWigFile(file=f) File bigwig_file.pyx, line 127, in bx.bbi.bigwig_file.BigWigFile.__init__ (lib/bx/bbi/bigwig_file.c:3011) File bbi_file.pyx, line 119,

Re: [galaxy-dev] tasks (parralelism) and from_work_dir bug

2013-04-14 Thread Jeremy Goecks
Hi, I have tried to use tasks with tophat2, but I got the following bug. multi.py +153 msg = 'nothing to merge for %s (expected %i files)' \ % (output_file_name, len(task_dirs)) This occurs because tophat2 tool uses from_work_dir feature to get the output

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