[galaxy-dev] [GSoC 2013] Introduction

[Saket Choudhary]

Hi Everyone!

I have been selected to work on the eQTL pipeline and visualisation for the
Galaxy Project as part of the Google Summer of Code 2013 (
http://www.google-melange.com/gsoc/homepage/google/gsoc2013)

I am pursuing my fourth year of undergraduate studies at Indian Institute
of Technology Bombay(http://www.iitb.ac.in/). My areas of interest are
broadly Bioinformatics and of lately I have been working on NGS problems.


I have created a blog here : http://galaxy-gsoc2013.blogspot.com/ . The
first post should be up soon.

My proposal is  here :
http://www.google-melange.com/gsoc/proposal/review/google/gsoc2013/saketkc/51001.
I would love to know your suggestions/comments.


I am relatively new to Galaxy, and some of my questions in the process
might be elementary, so kindly bear with it :)


Thanks

Saket Choudhary
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Re: [galaxy-dev] Multi File upload api

[Alex.Khassapov]

Thanks John,

We do have pretty old code, so I applied your patches.

One minor problem, in multi_upload tool "Dataset Name" is ignored, just picks 
the first file name. Do we need to update upoald.py or multi_upload.xml?

-Alex

-Original Message-
From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton
Sent: Friday, 31 May 2013 5:50 AM
To: Khassapov, Alex (CSIRO IM&T, Clayton)
Cc: Burdett, Neil (ICT Centre, Herston - RBWH); 
Subject: Re: Multi File upload api

Alex, if I am not mistaken you guys are using a fairly old version of the 
multiple file dataset code. I think on the server side you would need to apply 
the following three changesets to update the library backend to support the 
creation of multifile datasets (I guess if you are doing path pasting only the 
first changeset is really needed):

https://bitbucket.org/msiappdev/galaxy-extras/diff/lib/galaxy/webapps/galaxy/controllers/library_common.py?diff2=25e137130d32&at=stable
https://bitbucket.org/msiappdev/galaxy-extras/diff/lib/galaxy/webapps/galaxy/controllers/library_common.py?diff2=a15ce4c00716&at=stable
https://bitbucket.org/msiappdev/galaxy-extras/diff/lib/galaxy/webapps/galaxy/controllers/library_common.py?diff2=d2ae2265bc96&at=stable

If your version of Galaxy is likewise pretty old you will need pull request 123 
as first 
(https://bitbucket.org/galaxy/galaxy-central/pull-request/123/refactor-library_commonpy-toward-more/diff).

Once those are in place updating example_watch_folder.py should be pretty 
doable (Hagai Cohen had it working at some point):

1) You will need to replace:

data['upload_option'] = 'upload_paths'

with

data['upload_option'] = 'upload_paths_multifile'

2) You will need to specify a name (e.g. add something like:
data['NAME'] = os.path.basename(fullpath))

3) Multiple file datasets do not support data['ext'] = 'auto', so you will need 
to specify an explicit format there (the script will hopefully be able to 
determine this from the inputs).

The most updated version of the multiple file dataset stuff 
https://bitbucket.org/msiappdev/galaxy-extras/ paired with the most updated 
version of blend4j (https://github.com/jmchilton/blend4j) are compatible and if 
you do enough digging can provide insights on how to create multiple file 
datasets via the API (library path pastes, library server directory uploads, 
and history uploads).

Hope this helps,
-John

On Thu, May 30, 2013 at 1:40 AM,   wrote:
> Hi John,
>
>
>
> Can you please have a look at Neil's question.
>
>
>
> Thank you,
>
>
>
> -Alex
>
>
>
> From: Burdett, Neil (ICT Centre, Herston - RBWH)
> Sent: Thursday, 30 May 2013 4:30 PM
> To: Khassapov, Alex (CSIRO IM&T, Clayton)
> Subject: Multi File upload api
>
>
>
> Hi Alex,
>
>   The file "galaxy-dist/scripts/api/example_watch_folder.py" 
> allows us to watch a folder then upload files that arrive in a 
> specified input folder into the database and history.
>
>
>
> Can you ask your friend (who implemented the multi file upload tool), 
> what changes are necessary to this file so we can upload multiple 
> files as we do from the GUI. I assume he would know quite quickly what 
> to do and hopefully quite simple
>
>
>
> Thanks
>
> Neil

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[galaxy-dev] Making Public a Data Library Gives Internal Server Error

[Rodolfo Aramayo]

Hi,

As Admin, I uploaded a set of files from filesystems paths
Uploading is successful but when I try to make the datasets public I get
the following error:

Internal Server Error

Galaxy was unable to sucessfully complete your request  <==By The
Way...NOTE how sucessfully is misspelled!!

URL:
http://galaxy.tamu.edu/library_common/make_library_item_public?library_id=8115c1ef1d2e7998&show_deleted=False&item_type=ldda&cntrller=library_admin&use_panels=False&id=a29602c45f6f1217
File
'/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__
  return self.application(environ, start_response)
File
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
  return self.application(environ, start_response)
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
128 in __call__
  return self.handle_request( environ, start_response )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
184 in handle_request
  body = method( trans, **kwargs )
File
'/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/library_common.py',
line 1626 in make_library_item_public
  self._check_access( trans, cntrller, is_admin, ldda.library_dataset,
current_user_roles, use_panels, library_id, show_deleted )
AttributeError: 'NoneType' object has no attribute 'library_dataset'

Help will be appreciated

Thanks


--R
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Re: [galaxy-dev] Getting example_watch_folder.py to work...

[Hakeem Almabrazi]

Sorry for bringing this back but I am having an issue with the 
example_watch_folder.pl script.  After running in and put a fasta file, it gets 
copied over but it is empty.  Any idea how to fix this issue.

Uploaded by: galaxy@
Date uploaded: 2013-05-30
File size: 0 bytes
Data type: txt
Build: ?
Miscellaneous information: Uploaded temporary file (/tmp/API/myseq.fasta) does 
not exist.
empty
Database/Build: ?
Number of data lines: None
Disk file: /usr/local/galaxy/galaxy-dist/database/files/000/dataset_299.dat


Thank you for your help,

Regards
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Dannon Baker
Sent: Thursday, May 09, 2013 6:48 AM
To: neil.burd...@csiro.au
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] Getting example_watch_folder.py to work...

Hey Neil,

A user browsing that history wouldn't automatically get the updates (unless the 
history was already refreshing for some reason), but they definitely would upon 
refresh.  Glad you got the rest working!

-Dannon

On Thu, May 9, 2013 at 2:02 AM, 
mailto:neil.burd...@csiro.au>> wrote:
Hi all,
  I finally resolved the issue I'll mention it here to help anyone else 
who has the same issue. In "Edit" mode on the workflow you add the "Workflow 
control->Inputs" to use the api.

Final question
Everything gets created and stored in the database, but the history column on 
the left of the browser doesn't get updated. Can user see if the task has 
completed successfully and all files uploaded from the browser?

Thanks
Neil

From: Burdett, Neil (ICT Centre, Herston - RBWH)
Sent: Thursday, 9 May 2013 2:56 PM

To: galaxy-dev@lists.bx.psu.edu
Subject: Getting example_watch_folder.py to work...

Hi,

   I'm still struggling to get the example_watch_folder.py to work. So any 
help much appreciated.

I've created a simple workflow, which essentially opens a text file and then 
writes out the data to a html file.

My xml file:

  Test
  $__root_dir__/tools/copy/copy.pl
  --input_image "$inputImage"
  --output_html "$output"
  

  

  
  
http://tool.name>} on 
#echo os.path.basename( str ( $inputImage.name ) )#" />
  
  
Copy Tool

  


And copy.pl:
#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
my $input_image ;
my $output_html ;

# Get options from command line (i.e. galaxy)
my $result = GetOptions ( "input_image=s" => \$input_image,
  "output_html=s" => \$output_html )
  or die "Bad options";

print "input_image is: $input_image\n";

open FILE,"$input_image" or die $!;
my @lines = ;
close FILE;
my $numOfLines = scalar @lines;


# Create the output HTML, with links to the files and the square gif.
#
open HTML, ">", $output_html
or die "Failed to create output HTML file '$output_html': $! ";

print HTML<


iframe {
border: 0px;
background: #ee ;
}



Copy Files tool
Generated $numOfLines files
EOF

# Put direct links to each output file
foreach my $sub_filename ( @lines )
{
  print HTML "Direct link to the $sub_filename file.\n";
}

print HTML "\n";

print HTML "\n" ;

close HTML ;

So pretty basic.

I run:
./example_watch_folder.py cce1b01926646d548f6ddc32ff01aa2e 
http://140.253.78.234/galaxy/api/ /home/galaxy/data_input 
/home/galaxy/data_output "My API Import" f2db41e1fa331b3e

and get the following output:
{'outputs': ['a799d38679e985db'], 'history': '33b43b4e7093c91f'}

I can see the sample.txt file I placed in the /home/galaxy/data_input has been 
put into the database:
/home/galaxy/galaxy-dist/database/files/000/dataset_8.dat

and:
http://140.253.78.234/galaxy/api/libraries/f2db41e1fa331b3e/contents/1cd8e2f6b131e891
shows the file has been uploaded:

{

"data_type": "txt",

"date_uploaded": "2013-05-09T04:41:10.579602",

"file_name": "/home/galaxy/galaxy-dist/database/files/000/dataset_8.dat",

"file_size": 76,

"genome_build": "?",

"id": "1cd8e2f6b131e891",

"ldda_id": "1cd8e2f6b131e891",

"message": "",

"metadata_data_lines": 8,

"metadata_dbkey": "?",

"misc_blurb": "8 lines",

"misc_info": "uploaded txt file",

"model_class": "LibraryDataset",

"name": "sam2.txt",

"template_data": {},

"uploaded_by": "t...@test.com",

"uuid": null

}



However, looking in the histories:

http://140.253.78.234/galaxy/api/histories/33b43b4e7093c91f/contents/a799d38679e985db






The output file is zero as the input file can not be found as shown below in 
bold ...



{

"accessible": true,

"api_type": "file",

"data_type": "html",

"deleted": false,

"display_apps": [],

"display_types": [],

"download_url": 
"/galaxy/api/histories/33b43b4e7093c91f/contents/a799d38679e985db/display",

"file_ext": "html",

"file_name": "/home/galaxy/galaxy-dist/database/files/000/dataset_9.dat",

"file_size": 0,

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

[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 the CloudMap workflows that worked. But the second failes 
> with this error message:
> 
> Failed to open URL: 
> https://main.g2.bx.psu.edu/workflow/export_to_file?id=f444ce954bdc4953
> Exception: HTTP Error 500: Internal Server Error
> 
> I don't see any information in the log files.
> 
> regards, Andreas
> 
> On 22.05.2013 13:57, Dannon Baker wrote:
>> On Wed, May 22, 2013 at 3:12 AM, Andreas Kuntzagk 
>> > > wrote:
>> 
>>But how do I get the workflow_id? For example for the workflow
>>
>> https://main.g2.bx.psu.edu/u/__gm2123/w/cloudmap-unmapped-__mutant-workflow-no-candidates
>>
>> 
>> 
>>what would the workflow_id be?
>>(I tried "cloudmap-unmapped-mutant-__workflow-no-candidates" but this did 
>> not work.)
>> 
>> 
>> If you click on that link above, you can see the id in the url for the 
>> 'Import' link.  Again,
>> definitely not optimal -- public workflows should probably all be exposed 
>> via the API for use/import.
> 
> -- 
> Andreas Kuntzagk
> 
> SystemAdministrator
> 
> Berlin Institute for Medical Systems Biology at the
> Max-Delbrueck-Center for Molecular Medicine
> Robert-Roessle-Str. 10, 13125 Berlin, Germany
> 
> http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
> ___
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Re: [galaxy-dev] Multi File upload api

[John Chilton]

Alex, if I am not mistaken you guys are using a fairly old version of
the multiple file dataset code. I think on the server side you would
need to apply the following three changesets to update the library
backend to support the creation of multifile datasets (I guess if you
are doing path pasting only the first changeset is really needed):

https://bitbucket.org/msiappdev/galaxy-extras/diff/lib/galaxy/webapps/galaxy/controllers/library_common.py?diff2=25e137130d32&at=stable
https://bitbucket.org/msiappdev/galaxy-extras/diff/lib/galaxy/webapps/galaxy/controllers/library_common.py?diff2=a15ce4c00716&at=stable
https://bitbucket.org/msiappdev/galaxy-extras/diff/lib/galaxy/webapps/galaxy/controllers/library_common.py?diff2=d2ae2265bc96&at=stable

If your version of Galaxy is likewise pretty old you will need pull
request 123 as first
(https://bitbucket.org/galaxy/galaxy-central/pull-request/123/refactor-library_commonpy-toward-more/diff).

Once those are in place updating example_watch_folder.py should be
pretty doable (Hagai Cohen had it working at some point):

1) You will need to replace:

data['upload_option'] = 'upload_paths'

with

data['upload_option'] = 'upload_paths_multifile'

2) You will need to specify a name (e.g. add something like:
data['NAME'] = os.path.basename(fullpath))

3) Multiple file datasets do not support data['ext'] = 'auto', so you
will need to specify an explicit format there (the script will
hopefully be able to determine this from the inputs).

The most updated version of the multiple file dataset stuff
https://bitbucket.org/msiappdev/galaxy-extras/ paired with the most
updated version of blend4j (https://github.com/jmchilton/blend4j) are
compatible and if you do enough digging can provide insights on how to
create multiple file datasets via the API (library path pastes,
library server directory uploads, and history uploads).

Hope this helps,
-John

On Thu, May 30, 2013 at 1:40 AM,   wrote:
> Hi John,
>
>
>
> Can you please have a look at Neil’s question.
>
>
>
> Thank you,
>
>
>
> -Alex
>
>
>
> From: Burdett, Neil (ICT Centre, Herston - RBWH)
> Sent: Thursday, 30 May 2013 4:30 PM
> To: Khassapov, Alex (CSIRO IM&T, Clayton)
> Subject: Multi File upload api
>
>
>
> Hi Alex,
>
>   The file “galaxy-dist/scripts/api/example_watch_folder.py” allows
> us to watch a folder then upload files that arrive in a specified input
> folder into the database and history.
>
>
>
> Can you ask your friend (who implemented the multi file upload tool), what
> changes are necessary to this file so we can upload multiple files as we do
> from the GUI. I assume he would know quite quickly what to do and hopefully
> quite simple
>
>
>
> Thanks
>
> Neil

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Re: [galaxy-dev] BWA installation

[Carl Eberhard]

Hello, מירב

It looks like the indexing system/format in 'bwa index' has changed
and we haven't updated the wiki to reflect the changes.

The reverse index (which includes the .r* files) are now part of the
forward index. You
should be fine to proceed.

I'll update the wiki to reflect this.

>From https://github.com/lh3/bwa/blob/master/NEWS :

Release 0.5.10 and 0.6.0 (12 November, 2011)


The 0.6.0 release comes with two major changes. Firstly, the index
data structure has been changed to support genomes longer than 4GB.
The forward and reverse backward genome is now integrated in one
index.



On Thu, May 30, 2013 at 8:03 AM, מירב .  wrote:

> Hello all,
>
> I am trying to install BWA , I used the command:
>  " bwa index -a bwtsw /global_data/hg18full.fa " and I got only 5 files
> insted of 8
> The missing files are
>
>- rbwt
>- rpac
>- .rsa
>
> I didn't recieve any error message while running.
>
> thanks for your help
>
>
> merav
>
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Re: [galaxy-dev] Creating tool shed repository: installation of dependencies fails.

[Peter Cock]

On Thu, May 30, 2013 at 3:46 PM, Dave Bouvier  wrote:
> Peter,
>
> It turns out the issue was due to an overzealous firewall rule blocking
> outgoing FTP connections on the host running the automated tests. I've
> opened outgoing FTP and started a test for ncbi_blast_plus.
>
>--Dave B.

Thanks Dave - the download step has worked this time, but the
build failed with a BOOST dependency problem which is probably
best as a separate discussion.

Regards,

Peter
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Re: [galaxy-dev] Creating tool shed repository: installation of dependencies fails.

[Dave Bouvier]

Peter,

It turns out the issue was due to an overzealous firewall rule blocking 
outgoing FTP connections on the host running the automated tests. I've 
opened outgoing FTP and started a test for ncbi_blast_plus.


   --Dave B.

On 5/30/13 06:01:53.000, Peter Cock wrote:

On Thu, May 30, 2013 at 10:30 AM, Joachim Jacob | VIB |
 wrote:

Unfortunately, updating to the latest code (9320:47ddf167c9f1) does not
solve the problem.



I may be seeing the same issue on the Test Tool Shed, which
suggests a recent regression:

This is for the NCBI BLAST+ tools, attempting to compile from source:

Installation errors - no functional tests were run for any tools in
this changeset revision
TypeNameVersion
blast+  package 2.2.26+
Error
[Errno 2] No such file or directory:
'/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpOASYB_/tmpkEDmTH/ncbi-blast-2.2.26+-src.tar.gz'

http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/c1a6e5aefee0



 
 
 
 ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz
 cd c++ &&
./configure --prefix=$INSTALL_DIR && make && make
install
 
 $INSTALL_DIR/bin
 
 
 
 
Downloads and compiles BLAST+ from the NCBI, which assumes you have
all the required build dependencies installed. See:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
 
 


This was based on an older working tool_dependencies.xml file,
and other than the comments should match that currently on the
main tool shed, where it was working:
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/9dabbfd73c8a



 
 
 
 ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz
 cd c++ &&
./configure --prefix=$INSTALL_DIR && make && make
install
 
 $INSTALL_DIR/bin
 
 
 
 
These links provide information for building the NCBI Blast+ package
in most environments.

System requirements
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
 
 


Peter


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[galaxy-dev] Setting up Galaxy interface to motif finding software

[Tom Hait .]

Dear Galaxy developers,

I hope you could help me with the following issue.
I wish to use galaxy tools in our AMADEUS motif finding software:
http://acgt.cs.tau.ac.il/amadeus/
AMADEUS helps many users who wish to find motifs in their sequences.
AMADEUS has 2 limitations:
1. It can find motifs vs all organism's genome.
2. If the user don't want to find motif vs all organism's genome then The
user itself will have to supply the sequences for the motif finding
according to his chipSeq peaks he got.

We would like that the user won't be troubled with the second limitation by
adding locally\cloud Galaxy that downloads to AMADEUS the relevant
sequences (~3000 sequences)
according to the peaks locations from a BED file supplied by the user.

As I see it - the galaxy installation will have to follow the objectives:
1. Work on windows OS.
2. Can be installed in the user computer by a script in AMADEUS
3. downloading time of the relevant sequences (~3000) won't take above 1-2
minutes

I will appreciate if someone of you will guide me with the procedure and
advise me with the best way to work with Galaxy-AMADEUS interface.

Thanks,

Tom hait
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Re: [galaxy-dev] Internal Server Error during installation of ncbi_blast_plus

[Keilwagen, Jens]

Hi Peter,

thanks for your email. Regarding you questions

> The Galaxy team should be able to ask some more targeted questions, but
> how far did the process get? 

I get this errorimmediately after clicking on "Install to Galaxy".

> Were you asked about the dependencies
> (e.g. the blast_dataypes repository or the underlying BLAST+ binaries)?

No, but "blast_datatypes" is already installed.

> P.S. What kind of system are you using? 64 bit Linux? Mac OS X?

galaxy-dist$ more /proc/version
Linux version 2.6.32-5-amd64 (Debian 2.6.32-48squeeze1) (da...@debian.org) (gcc 
version 4.3.5 (Debian 4.3.5-4) ) #1 SMP Mon Feb 2
5 00:26:11 UTC 2013

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Re: [galaxy-dev] Internal Server Error during installation of ncbi_blast_plus

[Keilwagen, Jens]

Hi Greg,

here is what the paster.log says:

172.31.30.183 - - [30/May/2013:07:39:54 +0200] "GET 
/admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F
 HTTP/1.0" 302 - "http://galaxy.jki.bund.de/admin_toolshed/browse_tool_sheds"; 
"Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 Firefox/21.0"
172.31.30.183 - - [30/May/2013:07:40:17 +0200] "GET 
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a
 HTTP/1.0" 500 - 
"http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a";
 "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 Firefox/21.0"
Error - : too many values to unpack
URL: 
http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', 
line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File '/opt/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 
'/opt/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 '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128 in 
__call__
  return self.handle_request( environ, start_response )
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in 
handle_request
  body = method( trans, **kwargs )
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 231 
in decorator
  return func( self, trans, *args, **kwargs )
File 
'/opt/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 894 in prepare_for_install
  common_install_util.get_dependencies_for_repository( trans, tool_shed_url, 
repo_info_dict, includes_tool_dependencies )
File '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', line 
88 in get_dependencies_for_repository
  installed_rd, missing_rd = 
get_installed_and_missing_repository_dependencies_for_new_install( trans, 
repo_info_tuple )
File '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', line 
192 in get_installed_and_missing_repository_dependencies_for_new_install
  tool_shed, name, owner, changeset_revision = rd_tup
ValueError: too many values to unpack


CGI Variables
-
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
  HTTP_ACCEPT_ENCODING: 'gzip, deflate'
  HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
  HTTP_CACHE_CONTROL: 'max-age=0'
  HTTP_CONNECTION: 'keep-alive'
  HTTP_COOKIE: 
'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa'
  HTTP_HOST: 'galaxy.jki.bund.de'
  HTTP_REFERER: 
'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a'
  HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 
Firefox/21.0'
  HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
  HTTP_X_FORWARDED_FOR: '172.31.30.183'
  ORGINAL_REMOTE_ADDR: '172.16.20.52'
  PATH_INFO: '/admin_toolshed/prepare_for_install'
  QUERY_STRING: 
'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a'
  REMOTE_ADDR: '172.31.30.183'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '0.0.0.0'
  SERVER_PORT: '8080'
  SERVER_PROTOCOL: 'HTTP/1.0'


WSGI Variables
--
  application: 
  paste.cookies: (,
 
'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa')
  paste.expected_exceptions: []
  paste.httpexceptions: 
  paste.httpserver.thread_pool: 
  paste.parsed_querystring: ([('tool_shed_url', 
'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', '1d92ebdf7e8d466c'), 
('changeset_revisions', '9dabbfd73c8a')], 
'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a')
  paste.recursive.forward: 
  paste.recursive.include: 
  paste.recursive.include_app_iter: 
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: '6905bf7ac8eb11e297ec0050568d0b1f'
  webob._parsed_query_vars: (MultiDict([('tool_shed_url', 
'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', '1d92ebdf7e8d466c'), 
('changeset_revisions', '9dabbfd73c8a')]), 
'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a')
  wsgi process: 'Multithreaded'


However, installing other tools from the tool shed was no problem so far.

Best regards, Jens

> -Ursprüngliche Nachricht-
> Von: Greg Von 

[galaxy-dev] Information for Galaxy Event Horizon

[Sarah Maman]

Dear all,


Four days of training in genomics are occurring on our local instance of 
Galaxy (27-30 May).


This training session takes place at INRA, Toulouse Auzeville, France, 
as part of a collaboration between Sigenae (http://www.sigenae.org/) and 
GenoToul bioinformatics platform (http://bioinfo.genotoul.fr/).


This session is composed of four training days:

   *

 Galaxy first step

   *

 Reads alignment and SNP calling

   *

 RNAseq alignment and transcripts assemblies

   *

 sRNAseq



Do you think it is possible to list our training session in your "Galaxy 
Event Horizon"?


Sincerely,

Sarah Maman



--
 --*--
Sarah Maman
INRA - LGC - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel:   +33(0)5.61.28.57.08
Fax:   +33(0)5.61.28.57.53 
--*--


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Re: [galaxy-dev] Internal Server Error during installation of ncbi_blast_plus

[Greg Von Kuster]

Hello Jens,

It looks like your Galaxy instance is fairly old.  What version of Galaxy are 
you running?

Thanks,

Greg Von Kuster

On May 30, 2013, at 1:49 AM, Keilwagen, Jens wrote:

> Hi Greg,
> 
> here is what the paster.log says:
> 
> 172.31.30.183 - - [30/May/2013:07:39:54 +0200] "GET 
> /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F
>  HTTP/1.0" 302 - "http://galaxy.jki.bund.de/admin_toolshed/browse_tool_sheds"; 
> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 Firefox/21.0"
> 172.31.30.183 - - [30/May/2013:07:40:17 +0200] "GET 
> /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a
>  HTTP/1.0" 500 - 
> "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a";
>  "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 Firefox/21.0"
> Error - : too many values to unpack
> URL: 
> http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a
> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', 
> line 149 in __call__
>  app_iter = self.application(environ, sr_checker)
> File 
> '/opt/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 
> '/opt/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 '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128 in 
> __call__
>  return self.handle_request( environ, start_response )
> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in 
> handle_request
>  body = method( trans, **kwargs )
> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 231 
> in decorator
>  return func( self, trans, *args, **kwargs )
> File 
> '/opt/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
>  line 894 in prepare_for_install
>  common_install_util.get_dependencies_for_repository( trans, tool_shed_url, 
> repo_info_dict, includes_tool_dependencies )
> File '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', 
> line 88 in get_dependencies_for_repository
>  installed_rd, missing_rd = 
> get_installed_and_missing_repository_dependencies_for_new_install( trans, 
> repo_info_tuple )
> File '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', 
> line 192 in get_installed_and_missing_repository_dependencies_for_new_install
>  tool_shed, name, owner, changeset_revision = rd_tup
> ValueError: too many values to unpack
> 
> 
> CGI Variables
> -
>  CONTENT_LENGTH: '0'
>  HTTP_ACCEPT: 
> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
>  HTTP_ACCEPT_ENCODING: 'gzip, deflate'
>  HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
>  HTTP_CACHE_CONTROL: 'max-age=0'
>  HTTP_CONNECTION: 'keep-alive'
>  HTTP_COOKIE: 
> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa'
>  HTTP_HOST: 'galaxy.jki.bund.de'
>  HTTP_REFERER: 
> 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a'
>  HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) 
> Gecko/20100101 Firefox/21.0'
>  HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
>  HTTP_X_FORWARDED_FOR: '172.31.30.183'
>  ORGINAL_REMOTE_ADDR: '172.16.20.52'
>  PATH_INFO: '/admin_toolshed/prepare_for_install'
>  QUERY_STRING: 
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a'
>  REMOTE_ADDR: '172.31.30.183'
>  REQUEST_METHOD: 'GET'
>  SERVER_NAME: '0.0.0.0'
>  SERVER_PORT: '8080'
>  SERVER_PROTOCOL: 'HTTP/1.0'
> 
> 
> WSGI Variables
> --
>  application: 
>  paste.cookies: ( galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa'>,
>  
> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa')
>  paste.expected_exceptions: []
>  paste.httpexceptions:  0x8851bd0>
>  paste.httpserver.thread_pool:  0x87b2450>
>  paste.parsed_querystring: ([('tool_shed_url', 
> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', '1d92ebdf7e8d466c'), 
> ('changeset_revisions', '9dabbfd73c8a')], 
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a')
>  paste.recursive.forward: 
>  paste.recursive.include: 
>  paste.recursive.include_app_iter: 
>  paste.recursive.script_name: ''
>  paste.throw_errors: True
>  request_id: '6905bf7ac8eb11e297ec0050568d0b1f'
>  webob._parsed_query_vars: (MultiDict([('tool_shed_url', 
> 'http

Re: [galaxy-dev] Creating tool shed repository: installation of dependencies fails.

[Dave Bouvier]

I was also able to install the BLAST+ repository and tool dependency 
locally, which suggests that the automated testing environment is 
causing this issue. I'll have a look at that and update you.


   --Dave B.

On 5/30/13 08:45:27.000, Björn Grüning wrote:

Hi Peter,

is it also crashing for you locally? I was also able to install the
wrapper successfully. I'm just wondering if the testtoolshed is not
updated or if I have some nice local modifications left, that are worth
a pull request :)

Cheers,
Bjoern


On Thu, May 30, 2013 at 10:30 AM, Joachim Jacob | VIB |
 wrote:

Unfortunately, updating to the latest code (9320:47ddf167c9f1) does not
solve the problem.



I may be seeing the same issue on the Test Tool Shed, which
suggests a recent regression:

This is for the NCBI BLAST+ tools, attempting to compile from source:

Installation errors - no functional tests were run for any tools in
this changeset revision
TypeNameVersion
blast+  package 2.2.26+
Error
[Errno 2] No such file or directory:
'/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpOASYB_/tmpkEDmTH/ncbi-blast-2.2.26+-src.tar.gz'

http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/c1a6e5aefee0



 
 
 
 ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz
 cd c++ &&
./configure --prefix=$INSTALL_DIR && make && make
install
 
 $INSTALL_DIR/bin
 
 
 
 
Downloads and compiles BLAST+ from the NCBI, which assumes you have
all the required build dependencies installed. See:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
 
 


This was based on an older working tool_dependencies.xml file,
and other than the comments should match that currently on the
main tool shed, where it was working:
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/9dabbfd73c8a



 
 
 
 ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz
 cd c++ &&
./configure --prefix=$INSTALL_DIR && make && make
install
 
 $INSTALL_DIR/bin
 
 
 
 
These links provide information for building the NCBI Blast+ package
in most environments.

System requirements
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
 
 


Peter
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Re: [galaxy-dev] Creating tool shed repository: installation of dependencies fails.

[Björn Grüning]

Hi Peter,

is it also crashing for you locally? I was also able to install the
wrapper successfully. I'm just wondering if the testtoolshed is not
updated or if I have some nice local modifications left, that are worth
a pull request :)

Cheers,
Bjoern

> On Thu, May 30, 2013 at 10:30 AM, Joachim Jacob | VIB |
>  wrote:
> > Unfortunately, updating to the latest code (9320:47ddf167c9f1) does not
> > solve the problem.
> >
> 
> I may be seeing the same issue on the Test Tool Shed, which
> suggests a recent regression:
> 
> This is for the NCBI BLAST+ tools, attempting to compile from source:
> 
> Installation errors - no functional tests were run for any tools in
> this changeset revision
> Type  NameVersion
> blast+package 2.2.26+
> Error
> [Errno 2] No such file or directory:
> '/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpOASYB_/tmpkEDmTH/ncbi-blast-2.2.26+-src.tar.gz'
> 
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/c1a6e5aefee0
> 
> 
> 
> 
> 
> 
>  type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz
> cd c++ &&
> ./configure --prefix=$INSTALL_DIR && make && make
> install
> 
>  action="prepend_to">$INSTALL_DIR/bin
> 
> 
> 
> 
> Downloads and compiles BLAST+ from the NCBI, which assumes you have
> all the required build dependencies installed. See:
> http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
> 
> 
> 
> 
> This was based on an older working tool_dependencies.xml file,
> and other than the comments should match that currently on the
> main tool shed, where it was working:
> http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/9dabbfd73c8a
> 
> 
> 
> 
> 
> 
>  type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz
> cd c++ &&
> ./configure --prefix=$INSTALL_DIR && make && make
> install
> 
>  action="prepend_to">$INSTALL_DIR/bin
> 
> 
> 
> 
> These links provide information for building the NCBI Blast+ package
> in most environments.
> 
> System requirements
> http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
> 
> 
> 
> 
> Peter
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
> 
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[galaxy-dev] BWA installation

[מירב .]

Hello all,

I am trying to install BWA , I used the command:
 " bwa index -a bwtsw /global_data/hg18full.fa " and I got only 5 files
insted of 8
The missing files are

   - rbwt
   - rpac
   - .rsa

I didn't recieve any error message while running.

thanks for your help


merav
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Re: [galaxy-dev] Creating tool shed repository: installation of dependencies fails.

[Peter Cock]

On Thu, May 30, 2013 at 11:06 AM, Björn Grüning
 wrote:
> Hi Joachim,
>
> your definition is working fine for me (latest galaxy-central
> 9895:e3455a092882).
>
> If have uploaded it to this test repository:
> http://testtoolshed.g2.bx.psu.edu/view/bgruening/precommit_test
>
> ... and was able to install it. blat has no executable flag, so I needed
> to add chmod +x into the definition.
>
> The next Galaxy stable will be out in one week, afaik. At that time it
> will work :)
>
> Cheers,
> Björn

That makes sense - I've used 'naked' JAR files but they don't
seem to need the executable flag set.

Peter

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Re: [galaxy-dev] Creating tool shed repository: installation of dependencies fails.

[Björn Grüning]

Hi Joachim,

your definition is working fine for me (latest galaxy-central
9895:e3455a092882).

If have uploaded it to this test repository:
http://testtoolshed.g2.bx.psu.edu/view/bgruening/precommit_test

... and was able to install it. blat has no executable flag, so I needed
to add chmod +x into the definition.

The next Galaxy stable will be out in one week, afaik. At that time it
will work :)

Cheers,
Björn


> Unfortunately, updating to the latest code (9320:47ddf167c9f1) does not 
> solve the problem.
> 
> In Trello, this card  #584 was posted, mentioning installing compiled 
> binaries is not yet possible, apparently. This is what I experience I 
> believe.
> (BTW, the search bar at the top of Trello does not work for me - Galaxy 
> board is only pinned to my account, so I cannot apparently search that way)
> 
> Thanks,
> Joachim
> 
> Joachim Jacob
> Contact details: http://www.bits.vib.be/index.php/about/80-team
> 
> 
> On 05/29/2013 07:43 PM, Dave Bouvier wrote:
> > Joachim,
> >
> > I believe the behavior you're experiencing may be due to an issue that 
> > was fixed between 9320:47ddf167c9f1 and the current stable branch. I 
> > would recommend updating to the most recent stable branch of 
> > galaxy-central.
> >
> >--Dave B.
> >
> > On 5/29/13 09:30:37.000, Joachim Jacob | VIB | wrote:
> >> Strange. When I just wget that link in a terminal, do 'chmod +X blat'
> >> and ./blat, it just works fine.
> >> Could it be that the permissions need to be set by Galaxy?
> >>
> >> Version info of the Tool Shed:
> >> *
> >> [galaxy@galaxy galaxy-dist]$ hg summary
> >> parent: 9320:47ddf167c9f1 tip
> >>   Use Galaxy's ErrorMiddleware since Paste's doesn't return
> >> start_response.  Fixes downloading tarballs from the Tool Shed when
> >> use_debug = false.
> >> branch: stable
> >> commit: 5 modified, 271 unknown
> >> update: (current)
> >> [galaxy@galaxy galaxy-dist]$
> >> *
> >>
> >> Version info of the Galaxy integrating the tool shed repository:
> >> *
> >> parent: 9292:2cc8d10988e0 security_2013.04.08
> >>   Controllers/history: use get_history in switch_to_history
> >> branch: stable
> >> commit: 4 modified, 22 unknown (new branch head)
> >> update: 11 new changesets (update)
> >> *
> >>
> >> Cheers,
> >> Joachim
> >>
> >> Joachim Jacob
> >> Contact details: http://www.bits.vib.be/index.php/about/80-team
> >>
> >>
> >> On 05/29/2013 03:08 PM, Greg Von Kuster wrote:
> >>> Hello Joachim,
> >>>
> >>> This URL does not properly download blat.  The Firefox browser
> >>> determines it as a text file, while Safari displays it.  This is the
> >>> cause of the problem.  Is there a different URL to download blat that
> >>> actually downloads it as an archive os some kind?
> >>>
> >>>
> >>> Greg Von Kuster
> >>>
> >>>
> >>>
> >>>
> >>> On May 29, 2013, at 6:54 AM, Joachim Jacob | VIB | wrote:
> >>>
>  Hi all,
> 
>  I am building a wrapper around BLAT, and have put it locally in a
>  toolshed. However, the automatic installation of dependencies fails:
> 
>  *
>  Tool dependency installation error:
>  [Errno 2] No such file or directory:
>  '/home/galaxy/galaxy-dist/database/tmp/tmp2J7K_L/database/tmp/tmp2J7K_L/blat
>   
> 
> 
>  *
> 
>  Note that there is a strange duplication in the path. Furthermore, on
>  that Galaxy instance, the database is on /mnt/testgalaxydb/database
>  instead of path mentioned in the error.
> 
>  The tool_dependencies.xml matches the wrapper xml. blat is just
>  downloaded from its url.
> 
>  *
>  
>  
>  
>  
>  
>    type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat
>   
> 
> 
>  
>  blat
>  $INSTALL_DIR/bin
>  
>  
>    action="prepend_to">$INSTALL_DIR/bin
>  
>  
>  
>  
>  The BLAT binary for linux x86_64 is retrieved from UCSC.
>  
>  
>  
>  *
> 
>  Thanks for helping me further.
> 
>  Cheers,
>  Joachim
> 
>  -- 
>  Joachim Jacob
>  Contact details: http://www.bits.vib.be/index.php/about/80-team
> 
> 
>  ___
>  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:
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> 
>  To search Galaxy mailing lists use the unified search at:
>  http://galaxypr

Re: [galaxy-dev] Creating tool shed repository: installation of dependencies fails.

[Joachim Jacob | VIB |]

Hi Peter,

Yes, but your NCBI-blast executables were always packed in a tar.gz. 
The BLAT executable I want to use is just downloadable as such, without 
extracting needed. That's where it goes wrong.



Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team




On Thu 30 May 2013 11:52:54 AM CEST, Peter Cock wrote:

On Thu, May 30, 2013 at 10:30 AM, Joachim Jacob | VIB |
 wrote:

Unfortunately, updating to the latest code (9320:47ddf167c9f1) does not
solve the problem.

In Trello, this card  #584 was posted, mentioning installing compiled
binaries is not yet possible, apparently. This is what I experience I
believe.


I don't understand why that issue is open, this is possible.
https://trello.com/card/-/506338ce32ae458f6d15e4b3/584

e.g. I've successfully tested installing the pre-compiled NCBI
BLAST+ binaries as an alternative to local compilation:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus

See revision 19:c1a6e5aefee0 where I switched back to
compiling:
http://testtoolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=c1a6e5aefee0&id=c1542e8b1988898c


(BTW, the search bar at the top of Trello does not work for me - Galaxy
board is only pinned to my account, so I cannot apparently search that way)


Yes - sadly the best we can do as non-members is filter cards
(pop out panel on right hand side) but that only looks at the titles.

Peter



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Re: [galaxy-dev] Creating tool shed repository: installation of dependencies fails.

[Peter Cock]

On Thu, May 30, 2013 at 10:30 AM, Joachim Jacob | VIB |
 wrote:
> Unfortunately, updating to the latest code (9320:47ddf167c9f1) does not
> solve the problem.
>

I may be seeing the same issue on the Test Tool Shed, which
suggests a recent regression:

This is for the NCBI BLAST+ tools, attempting to compile from source:

Installation errors - no functional tests were run for any tools in
this changeset revision
TypeNameVersion
blast+  package 2.2.26+
Error
[Errno 2] No such file or directory:
'/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpOASYB_/tmpkEDmTH/ncbi-blast-2.2.26+-src.tar.gz'

http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/c1a6e5aefee0






ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz
cd c++ &&
./configure --prefix=$INSTALL_DIR && make && make
install

$INSTALL_DIR/bin




Downloads and compiles BLAST+ from the NCBI, which assumes you have
all the required build dependencies installed. See:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download




This was based on an older working tool_dependencies.xml file,
and other than the comments should match that currently on the
main tool shed, where it was working:
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/9dabbfd73c8a






ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz
cd c++ &&
./configure --prefix=$INSTALL_DIR && make && make
install

$INSTALL_DIR/bin




These links provide information for building the NCBI Blast+ package
in most environments.

System requirements
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download




Peter
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Re: [galaxy-dev] Creating tool shed repository: installation of dependencies fails.

[Peter Cock]

On Thu, May 30, 2013 at 10:30 AM, Joachim Jacob | VIB |
 wrote:
> Unfortunately, updating to the latest code (9320:47ddf167c9f1) does not
> solve the problem.
>
> In Trello, this card  #584 was posted, mentioning installing compiled
> binaries is not yet possible, apparently. This is what I experience I
> believe.

I don't understand why that issue is open, this is possible.
https://trello.com/card/-/506338ce32ae458f6d15e4b3/584

e.g. I've successfully tested installing the pre-compiled NCBI
BLAST+ binaries as an alternative to local compilation:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus

See revision 19:c1a6e5aefee0 where I switched back to
compiling:
http://testtoolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=c1a6e5aefee0&id=c1542e8b1988898c

> (BTW, the search bar at the top of Trello does not work for me - Galaxy
> board is only pinned to my account, so I cannot apparently search that way)

Yes - sadly the best we can do as non-members is filter cards
(pop out panel on right hand side) but that only looks at the titles.

Peter
___
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Re: [galaxy-dev] Creating tool shed repository: installation of dependencies fails.

[Joachim Jacob | VIB |]

Unfortunately, updating to the latest code (9320:47ddf167c9f1) does not 
solve the problem.


In Trello, this card  #584 was posted, mentioning installing compiled 
binaries is not yet possible, apparently. This is what I experience I 
believe.
(BTW, the search bar at the top of Trello does not work for me - Galaxy 
board is only pinned to my account, so I cannot apparently search that way)


Thanks,
Joachim

Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 05/29/2013 07:43 PM, Dave Bouvier wrote:

Joachim,

I believe the behavior you're experiencing may be due to an issue that 
was fixed between 9320:47ddf167c9f1 and the current stable branch. I 
would recommend updating to the most recent stable branch of 
galaxy-central.


   --Dave B.

On 5/29/13 09:30:37.000, Joachim Jacob | VIB | wrote:

Strange. When I just wget that link in a terminal, do 'chmod +X blat'
and ./blat, it just works fine.
Could it be that the permissions need to be set by Galaxy?

Version info of the Tool Shed:
*
[galaxy@galaxy galaxy-dist]$ hg summary
parent: 9320:47ddf167c9f1 tip
  Use Galaxy's ErrorMiddleware since Paste's doesn't return
start_response.  Fixes downloading tarballs from the Tool Shed when
use_debug = false.
branch: stable
commit: 5 modified, 271 unknown
update: (current)
[galaxy@galaxy galaxy-dist]$
*

Version info of the Galaxy integrating the tool shed repository:
*
parent: 9292:2cc8d10988e0 security_2013.04.08
  Controllers/history: use get_history in switch_to_history
branch: stable
commit: 4 modified, 22 unknown (new branch head)
update: 11 new changesets (update)
*

Cheers,
Joachim

Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 05/29/2013 03:08 PM, Greg Von Kuster wrote:

Hello Joachim,

This URL does not properly download blat.  The Firefox browser
determines it as a text file, while Safari displays it.  This is the
cause of the problem.  Is there a different URL to download blat that
actually downloads it as an archive os some kind?


Greg Von Kuster




On May 29, 2013, at 6:54 AM, Joachim Jacob | VIB | wrote:


Hi all,

I am building a wrapper around BLAT, and have put it locally in a
toolshed. However, the automatic installation of dependencies fails:

*
Tool dependency installation error:
[Errno 2] No such file or directory:
'/home/galaxy/galaxy-dist/database/tmp/tmp2J7K_L/database/tmp/tmp2J7K_L/blat 



*

Note that there is a strange duplication in the path. Furthermore, on
that Galaxy instance, the database is on /mnt/testgalaxydb/database
instead of path mentioned in the error.

The tool_dependencies.xml matches the wrapper xml. blat is just
downloaded from its url.

*





type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat 




blat
$INSTALL_DIR/bin


$INSTALL_DIR/bin




The BLAT binary for linux x86_64 is retrieved from UCSC.



*

Thanks for helping me further.

Cheers,
Joachim

--
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


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