Package/Module RPY
by Hayes, Curt
Hi there all,
I have searched previous posts, nothing since 2010. I have a local install (production config - postgres, etc - on CENTOS 6.5).
Does anyone have RPY working? I install via toolshed and the folder is empty, and shows missing dependencies.
>From Galaxy User:
Dataset generation errors
Dataset 81: Build base quality distribution on data 9
Tool execution generated the following error message:
Traceback (most recent call last):
File "/apps/galaxy/galaxy-dist/tools/metag_tools/short_reads_figure_score.py", line 12, in <module>
from rpy import *
ImportError: No module named rpy
I have attempted to download/install the scripts but they fail with multiple errors (most posts out there have a bad URL) - http://getgalaxyp.org/install.html says use: curl http://rpy.svn.sourceforge.net/viewvc/rpy/trunk/rpy/?view=tar > rpy.tar.gz
if you view that it redirects you to another URL.
Via shell: R is installed: R version 2.13.0 (2011-04-13)
Can someone provide me some help please to get it working via Galaxy? I understand it works in Central.
>From Toolshed:
Name
Version
Type
Installation status
rpy<http://seachildrenslinuxvm.cloudapp.net:8080/admin_toolshed/manage_reposi...>
1.0.3
package
Error
Toolshed Error:
In file included from src/rpymodule2110.c:51: src/RPy.h:56:20: error: Python.h: No such file or directory In file included from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:68, from /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14, from src/RPy.h:89, from src/rpymodule2110.c:51: /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/npy_common.h:79:2: error: #error Must use Python with unicode enabled. <truncated>
Thanks,
Curt
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8 years, 9 months
Check file before uploading
by Neil.Burdett＠csiro.au
Hi
When selecting a file or after clicking on "Execute" to upload a file is it possible to check the file is appropriate i.e. by checking file extension etc, before the file is actually uploaded and put into the database? So the user can't upload the wrong file/format
Thanks
Neil
Neil Burdett
Software Engineer | The Australian e-Health Research Centre
Computational Informatics
CSIRO
E: Neil.Burdett(a)csiro.au T: 07 3253 3626
Address: Level 5, UQ Health Science Building 901/16 Royal Brisbane and Women's Hospital, Herston, Brisbane, QLD, 4029
www.csiro.au | http://milxview.csiro.au
8 years, 9 months
Installing S-Mart on Mac SOX local instance
by Bernardo Bello
Hi,
I am having problems to install a tool from tool shed named S_MART on my
local Galaxy.
The reason to install S_MART is to use DETR'PROK in Galaxy.
Attached is the 'error' Galaxy indicates after installing some programs
from toolshed.
I've seen this related post, but I don't know if we are talking about the
same problem.<http://dev.list.galaxyproject.org/Problem-installing-tool-Galaxy-local-td...>
Here are the commands aI've used up to now:
Thanks
hg clone https://bitbucket.org/galaxy/galaxy-dist/
cd galaxy-dist
hg update stable
sh run.sh # gave errors, so see below
# solve problem at startup (
https://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg13354.html)
% export LC_ALL='en_US.UTF-8'
% sh run.sh
done # Go to http://localhost:8080/ and register as popnard(a)gmail.com
# Setup admin user (https://wiki.galaxyproject.org/Admin/Interface). To
give a user Galaxy admin privileges, add their Galaxy login ( email ) to
the list in the following config setting in the Galaxy configuration file
universe_wsgi.ini.
admin_users = popnard(a)gmail.com
# Set 'Tool Dependencies'
https://wiki.galaxyproject.org/Admin/Config/ToolDependencies?action=show&...
mkdir tool_dependency_dir
done # add tool dependencies folder to 'universe_wsgi.ini' -> Galaxy
provides a method for managing the dependencies of Galaxy tools installed
from the Tool Shed. In this case, it is simply necessary to set the
tool_dependency_dir option of universe_wsgi.ini to a path writable by the
Galaxy server.
done # restart server
First, I modified the universe_wsgi.ini file by removing the "#" before the
tool_config_file and tool_path lines. #
http://user.list.galaxyproject.org/Installing-new-tools-from-the-tool-she...
# Then, I created a shed_tools folder in my $HOME directory before
modifying the shed_tool_conf.xml file
<?xml version="1.0"?>
<toolbox tool_path="$HOME/shed_tools">
</toolbox>
done # INSTALL R
done # ADD R PACKAGES
R --slave --no-save --no-restore --quiet -e 'if("RColorBrewer" %in%
rownames(installed.packages()) == FALSE){install.packages("RColorBrewer",
repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}'
R --slave --no-save --no-restore --quiet -e 'if("Hmisc" %in%
rownames(installed.packages()) == FALSE){install.packages("Hmisc", repos =
c("http://cran.rstudio.com/"), dependencies = TRUE)}'
--
*Bernardo Bello Ortí*
PhD student
CReSA-IRTA
Campus de Bellaterra-Universitat Autònoma de Barcelona
Edifici CReSA
08193 Bellaterra (Barcelona, Spain)
Tel.: 647 42 52 63 *www.cresa.es <http://www.cresa.es> *
8 years, 9 months
krona to metaphlan patch
by Langhorst, Brad
I’m running with these local additions to Dannon’s metaphlan repo.
I think it would be better to add these to the current metaphlan repo than to release them standalone.
8 years, 9 months
extract_genomic_dna.py
by Adhemar
Hi,
In order to have the transcript_id for each sequence extracted from the
cuffmerge .gtf file I had to change the extract_genomic_dna.py by adding
the following lines after line 153:
attributes = gff_util.parse_gff_attributes( feature[8] )
if ( "transcript_id" in attributes ):
name = attributes.get( "transcript_id", None )
This way the variable name gets the transcript_id if it exists.
If it's correct, I would appreciate this modification in future galaxy
distributions.
Thanks!
Adhemar
8 years, 9 months
Problem with executing newly installed tools (via admin)
by Nicolas Cybulski
Ok,
a small update on this problem.
I have set up a local tool shed with in it a repository that holds 2
tool definitions of the same tool but with different verision nbrs
<tool id="NicybDummyTool" name="Nicyb Dummy Tool" version="1.0">
<description>Dummy Tool</description>
<command interpreter="python">
dummyTool.py $inputFile $operand $outputFile
</command>
<inputs>
<param name="inputFile" type="data" format="txt" label="Input txt
file" />
<param name="operand" type="text" size="2" label="Operand"/>
</inputs>
<outputs>
<!--callpeaks output-->
<data name="outputFile" format="txt" label="${tool.name}: output" />
</outputs>
<tests>
<test>
<param name="inputFile" value="dummyTool_input.txt" ftype="txt"/>
<param name="operand" value="2"/>
<output name="outputFile" file="dummyTool_output.txt"/>
</test>
</tests>
and:
<tool id="NicybDummyTool" name="Nicyb Dummy Tool" version="2.0">
<description>Dummy Tool v2</description>
<command interpreter="python">
dummyTool_v2.py $inputFile $operand $outputFile
</command>
<inputs>
<param name="inputFile" type="data" format="txt" label="Input txt
file" />
<param name="operand" type="text" size="2" label="Operand"/>
</inputs>
<outputs>
<!--callpeaks output-->
<data name="outputFile" format="txt" label="${tool.name}: output" />
</outputs>
<tests>
<test>
<param name="inputFile" value="dummyTool_input.txt" ftype="txt"/>
<param name="operand" value="2"/>
<output name="outputFile" file="dummyTool_output_v2.txt"/>
</test>
</tests>
</tool>
</tool>
I am successful in installing these tools in Galaxy using out own toolshed.
I get the following lines in shed_tool_conf.xml
<section id="nicyb_test_3" name="nicyb test 3" version="">
<tool
file="galaxy.psb.ugent.be/repos/nicyb/testbla2/4c7117d7f90d/testbla2/dummyTool_wrapper.xml"
guid="galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/1.0">
<tool_shed>galaxy.psb.ugent.be:3333/toolshed</tool_shed>
<repository_name>testbla2</repository_name>
<repository_owner>nicyb</repository_owner>
<installed_changeset_revision>4c7117d7f90d</installed_changeset_revision>
<id>galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/1.0</id>
<version>1.0</version>
</tool>
<tool
file="galaxy.psb.ugent.be/repos/nicyb/testbla2/4c7117d7f90d/testbla2/dummyTool_wrapper_v2.xml"
guid="galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/2.0">
<tool_shed>galaxy.psb.ugent.be:3333/toolshed</tool_shed>
<repository_name>testbla2</repository_name>
<repository_owner>nicyb</repository_owner>
<installed_changeset_revision>4c7117d7f90d</installed_changeset_revision>
<id>galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/2.0</id>
<version>2.0</version>
</tool>
</section>
When I look in the tool panel I can see both tools under section nicyb
test3.
Upon selecting one I get Nicyb Dummy Tool and then a drop down with
"version 1.0" and "version 2.0"
However, when I change the version nbrs I get the following error:
Module MySQLdb.connections:36 in defaulterrorhandler view
OperationalError: (OperationalError) (1241, 'Operand should contain 1
column(s)') 'INSERT INTO event (create_time, update_time, history_id,
user_id, message, session_id, tool_id) VALUES (%s, %s, %s, %s, %s, %s,
%s)' (datetime.datetime(2014, 4, 8, 14, 34, 48, 567645),
datetime.datetime(2014, 4, 8, 14, 34, 48, 567654), 1L, 1L, "Tool params:
{'operand': u'', 'tool_state':
u'800255db313334303737356537316139353463626339613333356235633261356166623236313166623137643a3762323236663730363537323631366536343232336132303232356332323465366636653635356332323232326332303232356635663730363136373635356635663232336132303330326332303232356635663732363537323735366535663732363536643631373035663661366636323566363936343566356632323361323036653735366336633263323032323639366537303735373434363639366336353232336132303232333233323232376471002e',
'refresh': u'refresh', 'inputFile': u'22'}", 16L,
[u'galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/2.0',
u'galaxy.psb.ugent.be:3333/toolshed/repos/nicyb/testbla2/NicybDummyTool/1.0'])
Is there anyone with similar experiences or an explanation for this ?
Kind regards,
Nicolas
On 04/02/2014 06:00 PM, galaxy-dev-request(a)lists.bx.psu.edu wrote:
> Subject:
> [galaxy-dev] Problem with executing newly installed tools (via admin)
> From:
> "Nicolas Cybulski" <nicyb(a)psb.vib-ugent.be>
> Date:
> 04/02/2014 10:38 AM
>
> To:
> galaxy-dev(a)lists.bx.psu.edu
>
>
> Hi,
>
> I have installed the Picard tools using the Tool-shed functionality in
> the admin tools.
> The tools and requisites have been correctly installed and run correctly.
> The insert statement to the event table fails however. I get the
> following error on screen:
>
> |OperationalError: (OperationalError) (1241, 'Operand should contain 1
> column(s)') 'INSERT INTO event (create_time, update_time, history_id,
> user_id, message, session_id, tool_id) VALUES (%s, %s, %s, %s, %s, %s,
> %s)' (datetime.datetime(2014, 4, 2, 9, 32, 47, 823142),
> datetime.datetime(2014, 4, 2, 9, 32, 47, 823170), 35L, 4L, "Tool
> params: {'histWidth': u'0', 'deviations': u'10.0', 'malevel':
> u'ALL_READS', 'input_file': u'5266', 'out_prefix': u'Insertion size
> metrics', 'refresh': u'refresh', 'minPct': u'0.05', 'tool_state':
> u'800254cf010000316164663833323133363237333739303833323639353065346362343762393730383966363664313a37623232363836393733373435373639363437343638323233613230323235633232333035633232323232633230323236343635373636393631373436393666366537333232336132303232356332323331333032653330356332323232326332303232363936653730373537343566363636393663363532323361323032323335333233363336323232633230323235663566373036313637363535663566323233613230333032633230323235663566373236353732373536653566373236353664363137303566366136663632356636393634356635663232336132303665373536633663326332303232366436313663363537363635366332323361323032323563323234313463346335663532343534313434353335633232323232633230323236663735373435663730373236353636363937383232336132303232356332323439366537333635373237343639366636653230373336393761363532303664363537343",
> 1468L,
> [u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0',
> u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0'])
>
> |The problem seems to be a duplicate entry of the tool_id
>
> |[u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0',
> u'toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0']
>
> |In the shed_tool_conf.xml the tools are generated as follows
>
> <tool
> file="toolshed.g2.bx.psu.edu/repos/devteam/picard/ab1f60c26526/picard/rgPicardI..."guid="toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0">
>
> If I change this guid to something less complicated like
>
> <tool
> file="toolshed.g2.bx.psu.edu/repos/devteam/picard/ab1f60c26526/picard/rgPicardI..."
> guid="testPicard">
>
> and restart galaxy it works ...
> for all tools (so not only the one that I've changed).
>
> Does anyone have an idea as to why this is ?
>
> kind regards,
>
> Nicolas
8 years, 9 months
patches to bjorn's bismark wrapper
by Langhorst, Brad
This patch updates bjorn’s bismark wrapper to work with latest bismark and allows methylation extraction from SAM or BAM files.
It no longer sorts the BAM from bismark (to allow methylation extraction to work).
8 years, 9 months
authorize non admin user to only link a directory of files
by Berner, Thomas
Hi,
we recently activated the feature for non admin users which allows them to upload a directory of files:
...
# Add an option to the library upload form which allows authorized
# non-administrators to upload a directory of files. The configured directory
# must contain sub-directories named the same as the non-admin user's Galaxy
# login ( email ). The non-admin user is restricted to uploading files or
# sub-directories of files contained in their directory.
#user_library_import_dir = None
user_library_import_dir = /opt/galaxy/galaxy-share/
...
However we would like to restrict the permission to only link to their files without copying them into galaxy, is this possible?
Greetings, Thomas
---
Thomas Berner
Julius Kühn-Institut (JKI)
- Federal Research Centre for Cultivated Plants - Erwin Baur-Straße 27
06484 Quedlinburg
- Germany -
Phone: ++49 ( 0 ) 3946 47 562
EMail: thomas.berner(a)jki.bund.de
8 years, 9 months
