Re: [galaxy-dev] galaxy cuffdiff running too long
Hello, When I install from binary files the boost problem doesn't go away and I get one extra error message in the beginning. Error running cuffdiff. cuffdiff: /usr/lib64/libz.so.1: no version information available (required by cuffdiff) [14:51:54] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [14:52:05] Inspecting maps and determining fragment length distributions. terminate called after throwing an instance of 'boost::exception_detail::clone_implboost::exception_detail::error_info_injectorboost::thread_resource_error ' what(): boost::thread_resource_error When I inspect the file libz.so.1 I get a symbolic link to another file, libz.so.1.2.3 which appears in the same directory. [@]# file /usr/lib/libz.so.1 /usr/lib/libz.so.1: symbolic link to `libz.so.1.2.3' [@]# file /usr/lib/libz.so.1.2.3 /usr/lib/libz.so.1.2.3: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), stripped -Rob On Mon, Jun 24, 2013 at 8:15 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote: 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 'boost::exception_detail::clone_implboost::exception_detail::error_info_injectorboost::thread_resource_error' what(): boost::thread_resource_error: Resource temporarily unavailable This is a linkage error with the Boost library; you might need to modify the Boost path and then recompile Cufflinks. That said, I don't recommend compiling from source unless needed; the Cufflinks suite is provided precompiled for many platforms. Getting the Cufflinks suite working and getting it working with Galaxy are two different things. I recommend: (a) getting Cufflinks working from the command line first using the tutorial: http://cufflinks.cbcb.umd.edu/tutorial.html (b) doing the tutorial in Galaxy; (c) using your own data with Cufflinks in Galaxy. Cufflinks can run very slow, especially if using a limited number of threads, so long running time is not necessarily an indication of error. Good luck, J. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] galaxy cuffdiff running too long
Hello, When we run cuffdiff from the command line we get this; [galaxy@q ~]$ /bin/cuffdiff /bin/cuffdiff: /usr/lib64/libz.so.1: no version information available (required by /bin/cuffdiff) cuffdiff v2.0.2 (3522) It looks like we are using a more recent version of cuffdiff than is supported by the galaxy tool wrappers (0.0.5 and 0.0.6). Using the 0.0.5 tool gives empty outputs. Using the 0.0.6 tool results in runs that last for five days without terminating. Has this behavior been seen before? How can we get good outputs to feed into cummeRbund? -Rob ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] UCSC Data Browser
Hello, Is anyone having trouble with the UCSC data browser? I got the following from one of my users: Hi guys, I try to fetch data from UCSC browser. A summary of my query shows that I am getting what I ask for, but when I Send the data to Galaxy I am returned to the channing galaxy home page and the data never appears in the history. When I use public instance, it all works. Not sure where the disconnect is. Thanks Any help would be appreciated. -Rob ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] UCSC Data Browser Not Working in Recent Release
Hello, I'm having some difficulty troubleshooting an error that one of our users found. When we select UCSC from Get Data We get a screen saying to submit query to galaxy but there are no other options and there is no connection to the UCSC website. Is this something other users have experienced? Is this the expected behaviour? -Rob ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Coupling the output of two tools
Hello, We added batch gfPcr as a tool in galaxy by writing a wrapper. We wrote another tool in python to modify the output of this tool (we increment the starts of the intervals by 1 to make the starting intervals 1 based) and wrote a wrapper for this other tool. Is is possible to couple these tools together as a single tool by writing a xml file? -Rob ___ 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] how to edit attributes of tool
Yes:) I meant to do it algorithmically though from within the code of the tool or the xml wrapper:) On Wed, Aug 15, 2012 at 7:10 PM, Ross ross.laza...@gmail.com wrote: Does clicking the info (i) icon on a history item help? On Wed, Aug 15, 2012 at 7:16 AM, Robert Chase re...@channing.harvard.eduwrote: Hello, Is there a way to annotate the notes of a custom tool to include information about the parameters passed to the tool? Let us say a user specifies a number n as a parameter to the tool. Is it possible to put this parameter in the notes that appear when the pencil icon is pressed? Reading the notes under the data tag set, wiki.g2.bx.psu.edu/Admin/Tools/Tool Config Syntax I didn't see any hint about how to pass the script parameters to the metadata boxes under the pencil icon. -Rob ___ 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; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] how to edit attributes of tool
Hello, Is there a way to annotate the notes of a custom tool to include information about the parameters passed to the tool? Let us say a user specifies a number n as a parameter to the tool. Is it possible to put this parameter in the notes that appear when the pencil icon is pressed? Reading the notes under the data tag set, wiki.g2.bx.psu.edu/Admin/Tools/Tool Config Syntax I didn't see any hint about how to pass the script parameters to the metadata boxes under the pencil icon. -Rob ___ 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] FastQC Tool Errors
Hello, We are having trouble running FastQC on our production server. The original stacktrace looked like this; Fastq failed. Error executing FastQC. Unknown option: djava.awt.headless Exception in thread main java.lang.NoClassDefFoundError: uk/ac/bbsrc/babraham/FastQC/FastQCApplication Caused by: java.lang.ClassNotFoundException: uk.ac.bbsrc.babraham.FastQC.FastQCApplication at java.net.URLClassLoader$1.run(URLClassLoader.java:200) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:188) at java.lang.ClassLoader.loadClass(ClassLoader.java:307) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:252) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320) Could not find the main class: uk.ac.bbsrc.babraham.FastQC.FastQCApplication. Program will exit. Then I tried to update java to the most current version. The current version is java -version java version 1.7.0_05 Java(TM) SE Runtime Environment (build 1.7.0_05-b06) Java HotSpot(TM) 64-Bit Server VM (build 23.1-b03, mixed mode) This changed the error message we got when we ran FastQC. The new trace looks like this; Fastq failed. Error executing FastQC. Unknown option: djava.awt.headless Error: Could not find or load main class uk.ac.bbsrc.babraham.FastQC.FastQCApplication The strange thing is that the tools works on our test server, which is almost an exact copy of the production server. -Rob __ Sure enough, this fixed the problem. I just installed the latest Sun JRE and it is working now. Thanks for the suggestion! I would have never guessed. -Josh On Mon, Jun 25, 2012 at 11:34 AM, simon andrews [hidden email]http://dev.list.galaxyproject.org/user/SendEmail.jtp?type=nodenode=4655462i=0 wrote: Yes, that's the broken version of gcj. I don't have a Centos machine here at the moment, but I think if you install OpenJDK and use the alternatives system to select that as the default JRE then that should fix things. Simon. On 25 Jun 2012, at 17:19, Josh Nielsen wrote: Hi Simon, I recently installed Java with the yum package manager on our compute nodes, and our cluster is a Centos 6 environment. Here is what the results of java -version returned on the compute nodes: *bash# java -version* *java version 1.5.0* *gij (GNU libgcj) version 4.4.4 20100726 (Red Hat 4.4.4-13)* * * *Copyright (C) 2007 Free Software Foundation, Inc.* *This is free software; see the source for copying conditions. There is NO* *warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE* . Is this version of Java too old? Perhaps I need to install the JRE manually? Thanks! On *Sat Jun 23 04:20:53 EDT 2012*, Simon Andrews [hidden email]http://dev.list.galaxyproject.org/user/SendEmail.jtp?type=nodenode=4655462i=1 wrote: Are you by any chance running an older version of gcj as your java version? There is a known bug in some of these where they don't correctly configure the headless environment, even if the correct parameters are passed. This causes exactly the kind of errors you're seeing. If this is the case you'll need to install a more recent JRE (or update your path to point to one which is already present). Simon. On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen [hidden email]http://dev.list.galaxyproject.org/user/SendEmail.jtp?type=nodenode=4655462i=2 wrote: Hello, I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output: Started analysis of Clip Approx 5% complete for Clip Approx 10% complete for Clip ... ... Approx 95% complete for Clip Approx 100% complete for Clip Analysis complete for Clip (.:9754): Gtk-WARNING **: cannot open display: And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this: Exception in thread main java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) at java.awt.Window.init(Window.java:437) at java.awt.Frame.init(Frame.java:419) at java.awt.Frame.init(Frame.java:384) at javax.swing.JFrame.init(JFrame.java:174) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.init(FastQCApplication.java:271) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102) Both errors seem to have something to do with the graphical GUI
Re: [galaxy-dev] bed files - The uploaded binary file contains inappropriate content
Hi Nate, I don't think that it does. We get the bed files from our GWAS pipelines. We were able to upload the file by adding 'bed' to the list of unsniffable_binary_formats in binary.py and manually specifying the format. Do you think this could cause problems later? -Rob On Thu, Jul 12, 2012 at 4:21 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 5, 2012, at 4:15 PM, Robert Chase wrote: Hello, We tried to upload a directory of files to our local data library and all uploads were successful except for one. The .bed file did not upload and gave an error message; The uploaded binary file contains inappropriate content. We would like to be able to share our data set with other researchers using galaxy but we need to be able to upload this bed file. Hi Rob, Is there any chance that the file contains Unicode? --nate -Rob ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] bed files - The uploaded binary file contains inappropriate content
Hello, We tried to upload a directory of files to our local data library and all uploads were successful except for one. The .bed file did not upload and gave an error message; The uploaded binary file contains inappropriate content. We would like to be able to share our data set with other researchers using galaxy but we need to be able to upload this bed file. -Rob ___ 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] Moving Data to New Instance
Hi Hans, Thankyou! I tried this; mysqldump -u galaxy_user -p galaxy db-name.out mysql -u galaxy_user -p galaxy db-name.out and it seemed to work:) I needed to run manage_db.sh to upgrade the schema but it ran without incident. All of the datasets in our old server now appear on our test server and I can download them into my history. -Rob On Wed, May 16, 2012 at 3:48 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: On 05/15/2012 05:42 PM, Robert Chase wrote: Hello All, We have a large amount of data on our production server that we would like to make available on our new test server. I tried to move data from our production server to our test server by copying the meta-data files and dataset files from ~/database/files to the new test server but it didn't work. Is there a way to move the datasets en mass? Hi Rob At the risk of repeating myself - sorry: You need a copy of your MySQL database for your new test instance of galaxy to connect to. what exactly does not work? what kind of error messages do you get? Regards, Hans -Rob __**_ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Migrating Workflows and Other Data to New Galaxy Instance
Hello, We have an existing galaxy instance that uses MySQL, has workflows and data libraries and countless changes to the source code and tools. We would like to save the database, workflows and data libraries but bring all the sourcecode up to date with the standard galaxy code. Because over 3000 of our files have been changed, we do not believe that we can realistically run hg update and then hg merge. We have built a test instance of galaxy that runs on a different virtual machine. One thought is to clone it, migrate all the datasets to it and then use the clone as the new production instance. One specific piece of information would be very helpful. Can we just copy the ~/data files to the test instance and have galaxy recognize them or is there metadata stored in the database? -Rob On Wed, Mar 28, 2012 at 10:16 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Rob I don't know what exactly you mean by new server. Assuming you are just talking about different hardware: Have you considered moving 'everything' to the new server? ie copying the Galaxy directory tree (especially make sure you copy ~/database/ ) and connect to the same PostgreSQL (or MySQL) database. If you want, I can give you more details how we successfully changed the hardware of our server last year Regards, Hans On 03/28/2012 03:31 PM, Robert Chase wrote: Thank you that could be very helpful to our users if we can't download them all as one big batch. I was hoping to be able to do something to save the users the headache of having to export and upload their workflows to the new server. Regards, -Rob On Wed, Mar 28, 2012 at 4:07 AM, Hans-Rudolf Hotz h...@fmi.ch mailto:h...@fmi.ch wrote: Hi Robert Have you looked at the Download or Export option? - you get this option, when you click on the triangle next to the names of you workflows. Regards, Hans On 03/27/2012 08:36 PM, Robert Chase wrote: Hello, We are going to migrate to a new instance of the galaxy server. Our current instance contains a number of workflows and other data that we would like to have available on the new server. Is there a way to backup the workflows and then reload them on the new server? Regards, -Robert Paul Chase Channing Lab __**__**_ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Workflow import error
Hello Dannon,
I have downloaded the fastqc compiled program from
http://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc
I have added the directory containing the program fastqc to the path. The
source version gave an error.
Now I can successfully run the fastqc tool from the tool menu. I got this
tool (the xml and python file) from the repository
http://toolshed.g2.bx.psu.edu/repos/jjohnson/fastqc
I tried deleting the uploaded workflow and uploading it again. I still get
a screen complaining that it requires tools that are not available. When I
click on the button for the tools, it says that fastqc is not available.
The operative part of the .ga file is here I think:
tool_id: fastqc,
tool_state: {\__page__\: 0, \contaminants\: \null\,
\chrom
Info\:
/galaxy/home/g2main/galaxy_main/tool-data/shared/ucsc/chrom/hg19.l
en, \out_prefix\: FastQC, \input_file\: \null\},
tool_version: 0.4,
When I look at the fastqc tool xml file I see that the version is 1.0.0
tool id=FastQC name=FastQC version=1.0.0
descriptionquality control checks on raw sequence data/description
command interpreter=pythonfastqc.py
Could it be a version problem? Does the capitalization of the tool id
matter?
-Rob
On Mon, Apr 16, 2012 at 9:31 PM, Dannon Baker dannonba...@me.com wrote:
Robert,
It sounds like you're experiencing two separate problems to me. Let's
isolating the problem to just the FastQC tool install, first, and move on
from there. There is a FastQC tool in your toolbar, and execution results
in the error you describe in the previous email of 'Fastq failed. Error
executing FastQC. /bin/sh: fastqc command not found'. Correct?
If this is the case, can you verify that you do have fastqc installed and
accessible on the path of the galaxy user? And, how did you add the tool
to galaxy- via toolshed or did you use the FastQC wrapper included with the
primary Galaxy distribution?
-Dannon
On Apr 16, 2012, at 6:23 PM, Greg Von Kuster wrote:
Hi Robert,
I've cc'd the galaxy-dev list on this reply since the workflow
components are primarily supported by other Galaxy development team members
and I'm not optimally suited to handle this issue. Please keep responses
on the galaxy-dev mail list so others that are interested can follow the
entire thread. You should receive a response on this soon.
Thanks for sending your messages,
Greg Von Kuster
On Apr 16, 2012, at 5:53 PM, Robert Chase wrote:
Hi Greg,
When I upload my workload ga file to galaxy, I get a screen saying that
some of the tools in the workflow are not available in this instance of
galaxy, specifically fastqc. I downloaded fastqc into my tools directory
and restarted galaxy, but when I tried to re-upload the workflow it
complained again that fastqc wasn't available. Fastqc does in fact load in
the tools sidebar, but when I try to run it I get the following:
An error occurred running this job: Fastq failed.
Error executing FastQC. /bin/sh: fastqc: command not found
-Rob
On Mon, Apr 16, 2012 at 10:21 AM, Greg Von Kuster g...@bx.psu.edu
wrote:
Hi Rob,
When you import a workflow into a Galaxy instance, the instance must
have all tools required by the workflow available in its tool panel. I've
only seen this error when the workflow requires a tool that is not
available, so can you let us know if this is the case?
Thanks,
Greg Von Kuster
On Apr 16, 2012, at 10:07 AM, Robert Chase wrote:
Hi Greg,
After I modified the modules.py file that bug went away, but now I'm
getting a new error:
Module galaxy.web.base.controller:420 in get_stored_workflow_steps
view
module = module_factory.from_workflow_step( trans,
step )
#Check if tool was upgraded
step.upgrade_messages =
module.check_and_update_state()
# Any connected input needs to have value
DummyDataset (these
# are not persisted so we need to do it every
time) step.upgrade_messages = module.check_and_update_state()
AttributeError: 'NoneType' object has no attribute
'check_and_update_state'
-Rob
On Mon, Apr 16, 2012 at 9:19 AM, Robert Chase
re...@channing.harvard.edu wrote:
Thanks Greg,
I'll try to merge the change into my version.
-Rob
On Mon, Apr 16, 2012 at 9:18 AM, Greg Von Kuster g...@bx.psu.edu
wrote:
Hello Robert,
Thanks for reporting this issue - it has been fixed in change set
7038:1fdcce63a06f, which is currently available only in our central
repository. It will be available in the dist in the next update.
Greg 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
following code diff shows the introduction of the line
tool_version = self.__get_tool_version( trans, tool_id )
but if you
[galaxy-dev] Workflow import error
Hello All, I have just tried to import a workflow file and when I try to view the workflow, I'm getting an error, global name 'self' is not defined. Error Traceback: View as: Interactivehttp://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# (full) http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# | Text http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# (full) http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# | XML http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# (full) http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# ⇝ NameError: global name 'self' is not defined clear this clear this URL: http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e Module weberror.evalexception.middleware:*364* in respond http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# view http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# *try**:* __traceback_supplement__ *=* errormiddleware*.*Supplement*,* self*,* environ app_iter *=* self*.*application*(*environ*,* detect_start_response*)* *try**:* return_iter *=* list*(*app_iter*)* http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#app_iter *=* self*.*application*(*environ*,* detect_start_response*)* Module paste.debug.prints:*98* in __call__ http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# view http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# *try**:* status*,* headers*,* body *=* wsgilib*.*intercept_output*(* environ*,* self*.*app*)* *if* status *is* None*:* # Some error occurred http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#environ*, * self*.*app*)* Module paste.wsgilib:*539* in intercept_output http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# view http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter) http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*80* in __call__ http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# view http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# environ*[*'paste.recursive.script_name'*]* *=* my_script_name *try**:* *return* self*.*application*(*environ*,* start_response*)* *except* ForwardRequestException*,* e*:* middleware *=* CheckForRecursionMiddleware*(* http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#*return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*632* in __call__ http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# view http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# *[**]**)**.*append*(*HTTPException*)* *try**:* *return* self*.*application*(*environ*,* start_response*)* *except* HTTPException*,* exc*:* *return* exc*(*environ*,* start_response*)* http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#*return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*160* in __call__ http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# view http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# kwargs*.*pop*(* '_'*,* None *)* *try**:* body *=* method*(* trans*,* kwargs *)* *except* Exception*,* e*:* body *=* self*.*handle_controller_exception*(* e*,* trans*,* kwargs *)* http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#body *=* method*(* trans*,* kwargs *)* Module galaxy.web.controllers.workflow:*207* in display_by_id http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# view http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e# # Get workflow. stored_workflow = self.get_stored_workflow( trans, id ) return self.display(trans, stored_workflow) def display(self, trans, stored_workflow): http://127.0.0.1:8080/workflow/display_by_id?id=f2db41e1fa331b3e#*return* self*.*display*(*trans*,*
Re: [galaxy-dev] Workflow import error
Hello All, I'm pretty sure I found a bug in the main galaxy distribution. The following code diff shows the introduction of the line tool_version = self.__get_tool_version( trans, tool_id ) but if you look at the function definition containing that line, you see def from_workflow_step( Class, trans, step ): which does not half a self in it. Then we get an error. https://bitbucket.org/galaxy/galaxy-dist/diff/lib/galaxy/workflow/modules.py?diff2=e6464387ed3fdiff1=c60760713d26 -Rob ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] GATK tools
Hello, One of our users has been using the GATK (beta) tools on the main instance of galaxy and would like to have them locally accessible. I have looked at the main toolshed but I couldn't find them there. Is there a place I can download the GATK files and xml files? -Rob ___ 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] Problem uploading files from filesystem paths
Hello, I set the library_import_dir setting in my universe_wsgi.ini file so that I could upload a directory of files into galaxy. I'm getting the following error screen when I attempt the upload from /tmp. The permissions are that galaxy owns the files in /tmp. I get the same error message when I try to upload the files from my computer. -rw-r--r-- 1 galaxy stapusr 656960285 Apr 10 14:36 117681r.bam Uploaded by:re...@channing.harvard.edu Date uploaded:2012-04-10 File size:626.5 Mb Data type:auto Build:? Miscellaneous information:uploaded bam fileTraceback (most recent call last): File /share/shared/galaxy-central-hbc/tools/data_source/upload.py, line 410, in __main__() File /share/shared/galaxy-central-hbc/tools/data_source/upload.py, line 399, in __main__ Job Standard Error Traceback (most recent call last): File /share/shared/galaxy-central-hbc/tools/data_source/upload.py, line 410, in __main__() File /share/shared/galaxy-central-hbc/tools/data_source/upload.py, line 399, in __main__ add_file( dataset, registry, json_file, output_path ) File /share/shared/galaxy-central-hbc/tools/data_source/upload.py, line 338, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File /share/shared/galaxy-central-hbc/lib/galaxy/datatypes/binary.py, line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File /share/shared/galaxy-central-hbc/lib/galaxy/datatypes/binary.py, line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File /usr/local/python27/lib/python2.7/subprocess.py, line 672, in __init__ errread, errwrite) File /usr/local/python27/lib/python2.7/subprocess.py, line 1202, in _execute_child raise child_exception OSError: [Errno 13] Permission denied error Database/Build:? Number of data lines:None Disk file:/share/shared/galaxy-central-hbc/database/files/000/dataset_40.dat ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] An error occurred running this job: Args must match #! line at /PATHTOGALAXY/galaxy-central-hbc/tools/filters/fixedValueColumn.pl line 1.
Hello, When we try to add a column to a dataset we get the following error: An error occurred running this job: *Args must match #! line at /share/shared/galaxy-central-hbc/tools/filters/fixedValueColumn.pl line 1. * Perl documentation says this; (F) The setuid emulator requires that the arguments Perl was invoked with match the arguments specified on the #! line. Since some systems impose a one-argument limit on the #! line, try combining switches; for example, turn -w -U into -wU. It works on our development instance without error. -Robert Chase ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Tasks do not start
Hello, On our test instance of galaxy we have set up filesharing with the rest of our cluster. We have also setup LDAP authentication on the server. We are having problems getting data from the tools based on data_source.py. For instance, if we try to run ucsc main then we can click on get output and then send query to galaxy we do not get a green screen saying that our task has started, we are redirected right back to the welcome screen. No tasks appear in our history. Has anyone encountered this before? -Rob ___ 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] Migrating Workflows and Other Data to New Galaxy Instance
Thank you that could be very helpful to our users if we can't download them all as one big batch. I was hoping to be able to do something to save the users the headache of having to export and upload their workflows to the new server. Regards, -Rob On Wed, Mar 28, 2012 at 4:07 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Robert Have you looked at the Download or Export option? - you get this option, when you click on the triangle next to the names of you workflows. Regards, Hans On 03/27/2012 08:36 PM, Robert Chase wrote: Hello, We are going to migrate to a new instance of the galaxy server. Our current instance contains a number of workflows and other data that we would like to have available on the new server. Is there a way to backup the workflows and then reload them on the new server? Regards, -Robert Paul Chase Channing Lab __**_ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Migrating Workflows and Other Data to New Galaxy Instance
Hello, We are going to migrate to a new instance of the galaxy server. Our current instance contains a number of workflows and other data that we would like to have available on the new server. Is there a way to backup the workflows and then reload them on the new server? Regards, -Robert Paul Chase Channing Lab ___ 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/
