Create a package with binaries
by KRESS Arnaud (ESP)
Hi gentlemen,
I am currently struggling to create a custom package (to share via a toolshed) that would include a tool definition file and the associated binary. Once installed, I can launch a job but I get the following error message:
mytool.sh: line 14: mytool: unknown command
It seems that the PATH was not correctly set. What am I doing wrong ?
My directory tree in my package:
.
├── mytool.sh
├── mytool.xml
├── bin
│ └── mytool
└── tool_dependencies.xml
Here is my tool_dependencies.xml file content:
<?xml version="1.0"?>
<tool_dependency>
<package name="mytool" version="1.0">
<install version="1.0">
<actions>
<action type="set_environment">
<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
</action>
</actions>
</install>
<readme>
</readme>
</package>
</tool_dependency>
Thank you,
AK
5 years, 9 months
Problem with LWR (input size limitation)
by Misharl Monsoor
Hi everybody,
In our lab, we are trying to connect our Galaxy instance to a Windows 7
64 bits server, in order to executes programs that need to be run within
Windows. However we have a problem concerning the size of the input that
is uploaded to the Windows server, it doesn't accept inputs with a size
> 1.3 Gb ? We have the following problem with mmap function:
data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ)
error: [Errno 12] Cannot allocate memory
I have another question concerning the inputs, is there a way to use
several inputs that be uploaded to a Windows Server?
Thank you very much in advance,
Bests regards,
Cheers,
Misharl Monsoor
5 years, 9 months
Metadata error in uploading files to data libraries
by Jelle Scholtalbers
Hi all,
after an update to the following changeset(14859:7ba05957588a, stable,
05.12.14), our bam files that are uploaded(linked) to a data library, are
no longer indexed. The metadata_xxx.dat is created, but it stays empty.
The following error message appears in the log, although the state of the
dataset is 'ok':
galaxy.jobs WARNING 2014-12-05 12:47:02,218 Error accessing /g/K/K27.bam,
will retry: [Errno 1] Operation not permitted: '/g/K/K27.bam'
galaxy.jobs WARNING 2014-12-08 13:38:57,045 Error accessing /g/K/K2.bam,
will retry: [Errno 1] Operation not permitted: '/g/K/K2.bam'
All file permissions are correct (i.e. galaxy owns them). Furthermore,
executing samtools index, just works on those files:
samtools index /g/K/K2.bam
/g/galaxy/galaxy_data/files/_metadata_files/006/metadata_6598.dat
When uploading the file - "copy files into galaxy" - the samtools index
just works.
==============
Now, on a clean local install(14874:885f940bff64, stable, 05.12.14) and
samtools installed globally and with the bam file sorted, I get the
following situation:
When I try to upload this bam to a data library by linking the following
error is shown on the dataset (note: here the dataset is set in error
state, which does not happen on our server)
Uploaded by: scholtal(a)embl.de
Date uploaded: Mon Dec 8 17:42:39 2014 (UTC)
File size: 2.6 GB
UUID: d23cf11a-0372-41cb-939a-7c8761d78b73
Data type: auto
Build: ?
Miscellaneous information: Traceback (most recent call last): File
"/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
line 407, in __main__() File
"/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
line 396, in _
Job Standard Error
Traceback (most recent call last):
File
"/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
line 407, in
__main__()
File
"/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
line 396, in __main__
add_file( dataset, registry, json_file, output_path )
File
"/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
line 294, in add_file
if datatype.dataset_content_needs_grooming( dataset.path ):
File
"/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
line 147, in dataset_content_needs_grooming
version = self._get_samtools_version()
File
"/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
line 129, in _get_samtools_version
output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
stdout=subprocess.PIPE ).communicate()[1]
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
line 711, in __init__
errread, errwrite)
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
line 1308, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
error
Database/Build: ?
Number of data lines: None
Disk file: /Users/scholtalbers/workspace/idr_data/WT1.sort.bam
===============================
When uploading the bam without linking, I see the following processes:
Upload->set meta->samtools index->'error state'
Miscellaneous information: uploaded bam file Traceback (most recent call
last): File
"/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
line 407, in __main__() File
"/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.p
Job Standard Error
Traceback (most recent call last):
File
"/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
line 407, in
__main__()
File
"/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
line 396, in __main__
add_file( dataset, registry, json_file, output_path )
File
"/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
line 324, in add_file
if link_data_only == 'copy_files' and
datatype.dataset_content_needs_grooming( output_path ):
File
"/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
line 147, in dataset_content_needs_grooming
version = self._get_samtools_version()
File
"/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
line 129, in _get_samtools_version
output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
stdout=subprocess.PIPE ).communicate()[1]
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
line 711, in __init__
errread, errwrite)
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
line 1308, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
error
Database/Build: ?
Number of data lines: None
Disk file:
/Users/scholtalbers/workspace/galaxy-dist-new/database/files/000/dataset_6.dat
=================================
Although the error messages are different, it might be related?
Cheers,
Jelle
5 years, 9 months
Re: [galaxy-dev] Allow wildcards in upload files from filesystem paths
by Ryan G
Thanks. It would be a nice feature. I don't have write permissions on the
filesystem where the fastq files are stored.
On Thu, Dec 18, 2014 at 4:08 PM, Martin Čech <emulatorer(a)gmail.com> wrote:
>
> Wildcards are not supported in library upload. Sorry.
>
> You can either specify one by one or you can just move the .log files
> outside of a folder for a bit. Once the fastqs are uploaded you can move
> them back.
>
> Martin
>
> On Thu Dec 18 2014 at 3:46:30 PM Ryan G <ngsbioinformatics(a)gmail.com>
> wrote:
>
>> I have a directory with a bunch of fastq files mixed with .log files. I
>> only want to upload the .fastq files. Do I have to specify each fastq file
>> separately or can I use '*.fastq'? I tried the later, but got the error
>> 'Invald paths'.
>> ___________________________________________________________
>> 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:
>> https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>
>
5 years, 9 months
Job wrapper object
by Alexandre Defelicibus
Hi all,
I'm developing some tools on my Galaxy instance and I need to get some
information about the job that a tool creates.
The question is, how can I have a job_wrapper object in my tool wrapper? I
tried to use the reserved variable $__app__, but I got errors.
I couldn't import and use the galaxy lib in order to get the job
information.
Could someone show me the correct way to do that, with some examples?
I appreciate all the help.
Best regards,
--
Alexandre Defelicibus
Mestrando em Bioengenharia
Programa de Pós-Graduação em Bioengenharia
Universidade de São Paulo - USP
5 years, 9 months
Allow wildcards in upload files from filesystem paths
by Ryan G
I have a directory with a bunch of fastq files mixed with .log files. I
only want to upload the .fastq files. Do I have to specify each fastq file
separately or can I use '*.fastq'? I tried the later, but got the error
'Invald paths'.
5 years, 9 months
HOWTO share tool parameter settings?
by Lukasse, Pieter
Hi,
Do we have a way (or plans) for sharing tool parameter settings in Galaxy?
I know the following workarounds :
* Share a history with all users: so users can import your step and do "rerun" to run on their own file with your settings
* Wrap the step in a workflow with all parameters set and publish this workflow: users can run this "workflow"
* Have a dummy tool to produce a settings file and allow the users to choose this file when running the real tool
* Use a conditional and many macros that are basically a copy of each other, only differing in the parameter values
But what I would like to have is a way to define bindings between a settings file and the parameters in the tool form. Any plans, ideas?
Thanks,
Pieter Lukasse
Wageningen UR, Plant Research International
Department of Bioinformatics (Bioscience)
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
T: +31-317481122;
M: +31-628189540;
skype: pieter.lukasse.wur
http://www.pri.wur.nl<http://www.pri.wur.nl/>
5 years, 9 months
Stop autoselecting in drop-down menus
by Aleksey Jironkin
Hi,
I was wondering if there is a way to prevent auto-selecting an option
for Running a workflow? Quiet often users (especially novices) would
re-run workflows without checking much the data that goes in thinking it
will be the same as before. But because the options in drop down menus
are auto-populated it seems the top option is always selected by
default. For example, previously we had a single fasta file as reference
and in the process of a workflow few other fasta files get generated.
they appear above the previous fasta in the selection, so without paying
attention people skip the input without really checking it.
Can we manually add a "blank" selection at the top to force users to
select something?
Alex
--
Dr Aleksey Jironkin
Bioinformatician
Bioinformatics Unit
Infectious Disease Informatics
Microbiologicy Services, Colindale
Public Health England
61 Colindale Avenue
London
NW9 5EQ
Aleksey.Jironkin(a)phe.gov.uk
Tel: 020 83 276610
www.gov.uk/phe Follow us on Twitter @PHE_uk
Protecting and improving the nation’s health
5 years, 9 months
Error when opening bowtie2 tool page
by Anna Terry
Hi,
I am getting an error page when I try to open the bowtie2 tool page (after
selecting older version 0.2 a54de7e658f7 from drop down on version 0.3
c1ec08cb34f9 page).
URL: http://....../tool_runner/index
File
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 107 in __call__
return self.app( environ, start_response )
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132
in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190
in handle_request
body = method( trans, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py',
line 90 in index
template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2136 in
handle_input
errors, params = self.__check_param_values( trans, expanded_incoming,
expanded_state, old_errors, process_state, history=history, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2251 in
__check_param_values
errors = self.update_state( trans, inputs, state.inputs, incoming,
old_errors=old_errors or {}, source=source )
File '/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2514 in
update_state
group_state = state[input.name]
KeyError: 'params'
I can't see anything that gives me a clue where to investigate further,
hopefully someone here knows?
I have tried updating to latest changeset, and have restarted a few times,
but still the same error.
Thanks in advance for help
Anna
5 years, 9 months
[Spam:*****] Re: How galaxy workflow work ?
by Bruijn, Freek de
I am also having problems using the Galaxy API, with a similar error message to the one reported by Bongsoo Park a few weeks ago (Uncaught exception in exposed API method). We noticed it a few days ago and have not found the cause yet. What we do know:
- the problem occurs on several Galaxy servers, including the main instance at https://usegalaxy.org/;
- the problem seems to occur whilte using BioBlend, blend4j, and api Python scripts;
- even some of the blend4j unit tests are failing.
One of my colleagues noticed a lot of changes in for example workflows.py (in lib/galaxy/webapps/galaxy/api): https://bitbucket.org/galaxy/galaxy-dist/annotate/579d211c2b0fa8ef4195930...
Did something change in the Galaxy API? Should we adjust the libraries and the programs that use them?
Cheers, Freek
________________________________________
From: galaxy-dev [galaxy-dev-bounces(a)lists.galaxyproject.org] on behalf of galaxy-dev-request(a)lists.galaxyproject.org [galaxy-dev-request(a)lists.galaxyproject.org]
Sent: Tuesday, December 16, 2014 18:00
To: galaxy-dev(a)lists.galaxyproject.org
Subject: galaxy-dev Digest, Vol 102, Issue 17
Send galaxy-dev mailing list submissions to
galaxy-dev(a)lists.galaxyproject.org
To subscribe or unsubscribe via the World Wide Web, visit
https://lists.galaxyproject.org/listinfo/galaxy-dev
or, via email, send a message with subject or body 'help' to
galaxy-dev-request(a)lists.galaxyproject.org
You can reach the person managing the list at
galaxy-dev-owner(a)lists.galaxyproject.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of galaxy-dev digest..."
HEY! This is important! If you reply to a thread in a digest, please
1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread.
2. Strip out everything else in the digest that is not part of the thread you are responding to.
Why?
1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative.
Today's Topics:
1. Re: How galaxy workflow work ? (John Chilton)
2. Re: Metadata error in uploading files to data libraries
(John Chilton)
3. Re: package_numpy_1_7 can't be installed (Wang, Yu)
4. Re: "join" produces an import error (Wang, Yu)
5. Re: package_numpy_1_7 can't be installed (Björn Grüning)
----------------------------------------------------------------------
Message: 1
Date: Mon, 15 Dec 2014 14:24:13 -0500
From: John Chilton <jmchilton(a)gmail.com>
To: Bongsoo Park <bxp12(a)psu.edu>
Cc: galaxy-dev <galaxy-dev(a)lists.bx.psu.edu>
Subject: Re: [galaxy-dev] How galaxy workflow work ?
Message-ID:
<CANwbokcggD3W7Tkyd5fy-9d6qedLT+ta1gzzmkfE1Apa2R8w1A(a)mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Somehow your user object is not being set. Are you sure you have
initialized bioblend with the correct API key? Do other operations
work with that key?
-John
On Wed, Dec 3, 2014 at 11:00 AM, Bongsoo Park <bxp12(a)psu.edu> wrote:
> Hi All,
>
> I faced a problem after I tested the Bio-Blend API. I cannot access the
> history anymore with the below error messages. Although, I tried
> installation from the scratch, but I got the same error message. Please let
> me know how to fix this problem. Thanks!
>
> (GALAXY User Interface)
>
> =======================================================
>
> "xhr": {
>
> "readyState": 4,
>
> "responseText": "{\"err_msg\": \"Uncaught exception in exposed API
> method:\", \"err_code\": 0}",
>
> "responseJSON": {
>
> "err_msg": "Uncaught exception in exposed API method:",
>
> "err_code": 0
>
> },
>
> "status": 500,
>
> "statusText": "Internal Server Error",
>
> "responseHeaders": {
>
> "Date": "Wed, 03 Dec 2014 15:50:02 GMT\r",
>
> "cache-control": "max-age=0,no-cache,no-store\r",
>
> "Server": "PasteWSGIServer/0.5 Python/2.7.8\r",
>
> "Connection": "close\r",
>
> "content-type": "application/json\r"
>
> }
>
> =======================================================
>
> I found the error message in the Galaxy instance shell interface.
>
> =======================================================
>
> galaxy.web.framework.decorators ERROR 2014-12-03 10:50:02,279 Uncaught
> exception in exposed API method:
>
> Traceback (most recent call last):
>
> File "/home/bxp12/galaxy-dist/lib/galaxy/web/framework/decorators.py",
> line 244, in decorator
>
> rval = func( self, trans, *args, **kwargs)
>
> File
> "/home/bxp12/galaxy-ist/lib/galaxy/webapps/galaxy/api/history_contents.py",
> line 76, in index
>
> and ( history_id == trans.security.encode_id( trans.history.id ) ) ):
>
> AttributeError: 'NoneType' object has no attribute 'id'
>
> =======================================================
>
> Best,
>
> Bongsoo
>
>
> ___________________________________________________________
> 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:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
------------------------------
Message: 2
Date: Mon, 15 Dec 2014 14:31:20 -0500
From: John Chilton <jmchilton(a)gmail.com>
To: Jelle Scholtalbers <j.scholtalbers(a)gmail.com>
Cc: galaxy-dev <galaxy-dev(a)lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Metadata error in uploading files to data
libraries
Message-ID:
<CANwbokdzjumt4abseN3b6rxOkaXH+9fB23+_OhqmUtFqnxbxWw(a)mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hello,
Sorry we haven't made progress on this - and thanks for creating a
Trello card (https://trello.com/c/tw75nq1U).
It looks like samtools is not on your path, can you use it from the
command-line? If not you should probably install it - I would suggest
install samtools 0.1.19 with homebrew (looks like you are a on Mac).
If you can run samtools from the command-line - can you do a which
`samtools` from your command-line and see where it is coming from and
then add that directory explicitly to your Galaxy PATH - say at the
top of run.sh in your Galaxy root (let me know if you need more
details on that).
-John
On Tue, Dec 9, 2014 at 3:02 AM, Jelle Scholtalbers
<j.scholtalbers(a)gmail.com> wrote:
> Hi all,
>
> after an update to the following changeset(14859:7ba05957588a, stable,
> 05.12.14), our bam files that are uploaded(linked) to a data library, are no
> longer indexed. The metadata_xxx.dat is created, but it stays empty.
> The following error message appears in the log, although the state of the
> dataset is 'ok':
>
> galaxy.jobs WARNING 2014-12-05 12:47:02,218 Error accessing /g/K/K27.bam,
> will retry: [Errno 1] Operation not permitted: '/g/K/K27.bam'
> galaxy.jobs WARNING 2014-12-08 13:38:57,045 Error accessing /g/K/K2.bam,
> will retry: [Errno 1] Operation not permitted: '/g/K/K2.bam'
>
> All file permissions are correct (i.e. galaxy owns them). Furthermore,
> executing samtools index, just works on those files:
> samtools index /g/K/K2.bam
> /g/galaxy/galaxy_data/files/_metadata_files/006/metadata_6598.dat
>
> When uploading the file - "copy files into galaxy" - the samtools index just
> works.
>
> ==============
>
> Now, on a clean local install(14874:885f940bff64, stable, 05.12.14) and
> samtools installed globally and with the bam file sorted, I get the
> following situation:
> When I try to upload this bam to a data library by linking the following
> error is shown on the dataset (note: here the dataset is set in error state,
> which does not happen on our server)
>
> Uploaded by: scholtal(a)embl.de
> Date uploaded: Mon Dec 8 17:42:39 2014 (UTC)
> File size: 2.6 GB
> UUID: d23cf11a-0372-41cb-939a-7c8761d78b73
> Data type: auto
> Build: ?
> Miscellaneous information: Traceback (most recent call last): File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 407, in __main__() File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 396, in _
> Job Standard Error
>
> Traceback (most recent call last):
> File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 407, in
> __main__()
> File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 396, in __main__
> add_file( dataset, registry, json_file, output_path )
> File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 294, in add_file
> if datatype.dataset_content_needs_grooming( dataset.path ):
> File
> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
> line 147, in dataset_content_needs_grooming
> version = self._get_samtools_version()
> File
> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
> line 129, in _get_samtools_version
> output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
> stdout=subprocess.PIPE ).communicate()[1]
> File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
> line 711, in __init__
> errread, errwrite)
> File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
> line 1308, in _execute_child
> raise child_exception
> OSError: [Errno 2] No such file or directory
>
> error
> Database/Build: ?
> Number of data lines: None
> Disk file: /Users/scholtalbers/workspace/idr_data/WT1.sort.bam
>
> ===============================
> When uploading the bam without linking, I see the following processes:
> Upload->set meta->samtools index->'error state'
>
> Miscellaneous information: uploaded bam file Traceback (most recent call
> last): File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 407, in __main__() File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.p
> Job Standard Error
>
> Traceback (most recent call last):
> File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 407, in
> __main__()
> File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 396, in __main__
> add_file( dataset, registry, json_file, output_path )
> File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 324, in add_file
> if link_data_only == 'copy_files' and
> datatype.dataset_content_needs_grooming( output_path ):
> File
> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
> line 147, in dataset_content_needs_grooming
> version = self._get_samtools_version()
> File
> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
> line 129, in _get_samtools_version
> output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
> stdout=subprocess.PIPE ).communicate()[1]
> File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
> line 711, in __init__
> errread, errwrite)
> File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
> line 1308, in _execute_child
> raise child_exception
> OSError: [Errno 2] No such file or directory
>
> error
> Database/Build: ?
> Number of data lines: None
> Disk file:
> /Users/scholtalbers/workspace/galaxy-dist-new/database/files/000/dataset_6.dat
>
> =================================
>
> Although the error messages are different, it might be related?
>
> Cheers,
>
> Jelle
>
> ___________________________________________________________
> 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:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
------------------------------
Message: 3
Date: Mon, 15 Dec 2014 17:16:41 +0000
From: "Wang, Yu" <Yu.Wang(a)lrz.de>
To: John Chilton <jmchilton(a)gmail.com>
Cc: "Wang, Yu" <Yu.Wang(a)lrz.de>, "galaxy-dev(a)lists.galaxyproject.org"
<galaxy-dev(a)lists.galaxyproject.org>
Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed
Message-ID:
<f4c6170a-5f28-4871-971b-2881fc739510(a)BADWLRZ-SW13MB1.ads.mwn.de>
Content-Type: text/plain; charset="utf-8"
Hi, John,thanks for your answer. I installed svnversion, and compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found.
I could install package_numpy_1_9 by using galaxy main tool shed. There is something wrong with package_numpy_1_7 on my environment.
Cheers,
Yu
di29her
wang(a)lrz.de<mailto:wang@lrz.de>
On 15 Dec 2014, at 16:12, John Chilton <jmchilton(a)gmail.com<mailto:jmchilton@gmail.com>> wrote:
Looks like this - https://github.com/clarete/curdling/issues/19
I think you somehow need to install the package svn on your machine - if you have root on that machine the command might be something like "sudo zypper install svn" or may it is "sudo zypper install subversion". If you don't have root on the machine I would ask the operating system maintainer or try to compile and install svn locally and make it available to Galaxy.
Hope this helps,
-John
On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu <Yu.Wang(a)lrz.de<mailto:Yu.Wang@lrz.de>> wrote:
Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got the following error.
Can anyone point what goes wrong here?
Error Running from numpy source directory.
/bin/sh: svnversion: command not found
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503: UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
warnings.warn(BlasNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506: UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
warnings.warn(BlasSrcNotFoundError.__doc__)
/bin/sh: svnversion: command not found
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
warnings.warn(LapackNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
warnings.warn(LapackSrcNotFoundError.__doc__)
error: must supply either home or prefix/exec-prefix -- not both
Cheers,
Yu
di29her
wang(a)lrz.de<mailto:wang@lrz.de>
___________________________________________________________
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
5 years, 9 months
