- galaxy-dev - lists.galaxyproject.org

Depth of Coverage (local galaxy __ CloudMap)
by Wang, Xiaofei 04 Apr '14

04 Apr '14

Dear there, I got this error when I run CloudMap EMS Variant Density Mapping workflow for Depth of Coverage on the local Galaxy instance on Mac. In fact, it works fine for Depth of Coverage when I run another workflow (Unmapped Mutant workflow) locally. I really appreciate you guys for helping me to figure out so many problems! Thanks a lot! Best, Xiaofei Traceback (most recent call last): File "/Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File "/Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy/jobs/__init__.py", line 652, in prepare if job.user is None and job.galaxy_session is None: File "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/attributes.py", line 168, in __get__ return self.impl.get(instance_state(instance),dict_) File "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/attributes.py", line 453, in get value = self.callable_(state, passive) File "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/strategies.py", line 508, in _load_for_state return self._emit_lazyload(session, state, ident_key) File "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/strategies.py", line 552, in _emit_lazyload return q._load_on_ident(ident_key) File "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py", line 2512, in _load_on_ident return q.one() File "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py", line 2184, in one ret = list(self) File "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py", line 2227, in __iter__ return self._execute_and_instances(context) File "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/orm/query.py", line 2242, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py", line 1449, in execute params) File "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py", line 1584, in _execute_clauseelement compiled_sql, distilled_params File "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py", line 1698, in _execute_context context) File "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/base.py", line 1691, in _execute_context context) File "/Users/xiaofeiwang/softwares/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-macosx-10.6-intel-ucs2.egg/sqlalchemy/engine/default.py", line 331, in do_execute cursor.execute(statement, parameters) OperationalError: (OperationalError) database is locked u'SELECT galaxy_user.id AS galaxy_user_id, galaxy_user.create_time AS galaxy_user_create_time, galaxy_user.update_time AS galaxy_user_update_time, galaxy_user.email AS galaxy_user_email, galaxy_user.username AS galaxy_user_username, galaxy_user.password AS galaxy_user_password, galaxy_user.external AS galaxy_user_external, galaxy_user.form_values_id AS galaxy_user_form_values_id, galaxy_user.deleted AS galaxy_user_deleted, galaxy_user.purged AS galaxy_user_purged, galaxy_user.disk_usage AS galaxy_user_disk_usage, galaxy_user.active AS galaxy_user_active, galaxy_user.activation_token AS galaxy_user_activation_token \nFROM galaxy_user \nWHERE galaxy_user.id = ?' (1,)

2 1

version of SAM-to-BAM (CloudMap)
by Wang, Xiaofei 04 Apr '14

04 Apr '14

Dear there, When I run CloudMap EMS Variant Density Mapping workflow (takes VCF of heterozygous and homozygous variants to subtract) (imported from uploaded file) on local Galaxy instance, I got this [X] , when I wanted to edit the workflow. Also, I got this The following tools are beinge executed with a different version from what was available when this workflow was last saved because the previous version is no longer available for use on this galaxy instance. To upgrade your workflow and dismiss this message simply edit the workflow and re-save it to update the stored tool version. * toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.2: using version '1.1.2' instead of version '1.1.3' indicated in this workflow. * ,when I wanted to run the workflow. I know it is the problem with version of SAM-to-BAM. But, when I searched the Tool sheds > Search and browse tool sheds, there is only version 1.1.4 for SAM-to-BAM. When I tried to edit the workflow from Workflow > ...> Edit, I did not find where could I change the version of SAM-to-BAM. When I clicked on SAM-to-BAM on the Workflow Canvas, it showed the version is 1.1.3 for it. Could you tell me which version do I need exactly, and how to figure out this? Thanks a lot! Best, Xiaofei

2 2

Download workflow from main Galaxy
by Wang, Xiaofei 04 Apr '14

04 Apr '14

Dear there, I tried to download workflow and import it into another my local Galaxy instance. But, when I downloaded and exported it from main Galaxy by "Download to File", it showed as below. Not Found The resource could not be found. No route for /u/w/imported-cloudmap-ems-variant-density-mapping-workflow-takes-vcf-of-heterozygous-and-homozygous-variants-to-subtract/json-download Then, I tried "URL for Importing to Another Galaxy Use this URL to import the workflow directly into another Galaxy server: https://usegalaxy.org/u//w/imported-cloudmap-ems-variant-density-mapping-wo… (Copy this URL into the box titled 'Workflow URL' in the Import Workflow page.)" , it showed Failed to open URL: https://usegalaxy.org/u//w/imported-cloudmap-ems-variant-density-mapping-wo… Exception: HTTP Error 404: Not Found What is the reason for this? Many thanks for helping me! Best, Xiaofei

2 2

Better descriptions in job history?
by Smithies, Russell 04 Apr '14

04 Apr '14

Not sure if I've overlooked a setting somewhere, but is it possible to customize or tweak the job descriptions that are displayed in the history? Eg. "Compute sequence length on data 1" isn't very descriptive, but if perhaps the annotation field or a description field could be added it would make identification much easier eg. "Compute sequence length on data 1 [Burkholderia pseudomallei K96243]" or even for datatypes that have a defined definition line, perhaps a mouse-over hover could be added with the accession or definition pulled from the input file? These mouse-over hovers are already used to identify the view, edit, and delete icons so no additional libraries wold be used. I could probably hack something up but thought it better to try and get the feature included. Any thoughts? Thanx, --Russell

3 3

The main Galaxy Tool Shed is now running the next-stable branch
by Greg Von Kuster 04 Apr '14

04 Apr '14

For those interested, The main Galaxy Tool Shed is now running the next-stable branch in preparation for the upcoming Galaxy release currently scheduled for about 2 weeks from now. We'll continue to update the Tool Shed as new changeset are pushed to the next-stable branch. We'll alert you wnen the main Tool Shed is updated to the stable branch when it is tagged for the next Galaxy release. As usual, the test Galaxy Tool Shed continues to track the default branch. Thanks! Greg Von Kuster

1 0

Reg: Issue while adding simple repository dependencies for custom tool
by Janaki Rama Rao Gollapudi 04 Apr '14

04 Apr '14

Hi, I have implemented a custom tool called 'barcode-parse' and uploaded this custom to into my local tool shed(which is running at http://localhost:9009) Also able to install this custom tool from galaxy. Then I have added simple repository dependency. I have created a xml file 'repository_dependencies.xml'. Then I created a new repository in the toolShed called 'Test' and uploaded all necessary files(.py, definition xml file and repository dependency xml file) into this repository. (I have created another repository called 'string_occurrence' and uploaded necessary files into toolShed which is used as dependency repository) <?xml version="1.0"?> <repositories description=""> <repository toolshed="http://localhost:9009" name="string_occurrence" owner="janakiram-t1" /> </repositories> I tried to install custom tool 'barcode-parse' from galaxy, but I got below error message. The repository dependency definitions for this repository are invalid and will be ignored. I followed the steps mentioned in the galaxy wiki<https://wiki.galaxyproject.org/SimpleRepositoryDependencies> Am I doing anything wrong? Please suggest me on this. Thanks, JanakiRam

3 18

Problem downloading large processed datasets : galaxy local instance
by Nilaksha Neththikumara 04 Apr '14

04 Apr '14

Hello all, I'm currently successfully running a pipeline for metagenomic analysis on my locally installed galaxy instance and everything seemed to good by far. But when I'm trying to download my processed blast xml output (I used blast+ wrappers for this) , by clicking the small disk button nothing happens. I tried several options. 1) clicked the 'disk' icon to initiate the downloading 2) right clicked the 'disk' icon and tried to use saved linked as, but a dialog box doesnot appear for saving 3) tried copying the link and used curl on bash terminal, but progress bar is stuck at 0%. I think this is happening because my blast output dataset is much larger (around ~10GB) , but if that's the case, how am I supposed to get the data out of galaxy any way?? Thank a lot in advance. Regards! Nilaksha

5 9

(some) Tabular files not displaying correctly
by Lukasse, Pieter 04 Apr '14

04 Apr '14

Hi , I have this strange thing on my Galaxy server where some tabular files display correctly in the central frame while others will just display as some kind of plain text file where the tabs are read as spaces...but when loading them in excel they work just fine! Has anyone seen this before and what would be the solution/workaround? Screenshots: Bad: [cid:image002.jpg@01CF3932.37E5D170] Good: [cid:image003.jpg@01CF3932.37E5D170] Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

3 7

known name outputs shown in /database/files but not in galaxy windows
by ANGELICA GOMEZ ROIG 04 Apr '14

04 Apr '14

I have made a wrapper that has a tool that giving it an input file, gives you two output files with known extension: .gem and .log I call the tool with a python file, and I pass it the input file and the two output file names for galaxy to show them, but when I look into de database/files/000/ i get four files: dataset_54.dat (my first declared output that it's empty) dataset_54.dat.gem (the output that throws the tool) dataset_54.dat.log (the other output file that throws the tool) dataset_55.dat (my second declared output that it's empty) So,what I'm getting in the galaxy interface is _54.dat and _55.dat, both empty, instead of _54.dat.gem and _54.dat.log that are the good ones. How can I fix these? Thanks

2 1

picard wrappers to support the rna-seq metrics and downsample sam tools?
by Brad Zeitner 03 Apr '14

03 Apr '14

I saw from: http://dev.list.galaxyproject.org/contributing-patches-to-toolshed-repos-td… that B. Langhorst had submitted a change to the picard wrapper to support the rna-seq metrics - has that patch made it into any of the repo's? I'm not seeing it when I install the picard wrappers. I'd prefer not having to manually apply that patch to get the support for running rna-seq metrics. -Brad Zeitner ________________________________ --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org

2 1