Re: [galaxy-dev] [galaxy-user] Blast2GO local instance Re: Table with gene count reads

2012-04-03 Thread Peter Cock
On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster g...@bx.psu.edu wrote:

 On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:

 Have you seen the README file that comes with the
 Blast2GO wrapper? Perhaps the 'install from toolshed'
 could be tweaked to make this kind of documentation
 more visible...

 If you are installing a single repository that contains a file named one of
 (case is ignored) readme, readme.txt, read_me, read_me.txt, the contents of
 the file will be displayed on the tool panel section selection page.  An
 example using the antismash repository on the main tool shed is below.  This
 new feature is available in change set revision 6945:5ea04ccb61e8, which is
 currently running on the Galaxy tool shed and our central development
 repository.  It will be available in the next Galaxy distribution.

Great. In this case I've actually called the file blast2go.txt (to match
the use of blast2go.xml and blast2go.py). I didn't want to use a
generic name like README since there could be other tools
installed in the same folder (this predates the auto-install system).
Is this naming pattern common used enough to justify including in
the Galaxy Tool Shed code for spotting a README file?

 Care must be taken when following instructions in README files since some of
 the information may be outdated.  For example, the Galaxy functional test
 framework was recently enhanced to support testing tools included in
 installed repositories, but I've seen some README files currently in
 repositories that instruct installers to move test data to the Galaxy
 installation environment, which is no longer necessary.

Some of my tools' README files will need a little clarification following
those changes to Galaxy.

Thanks,

Peter

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Re: [galaxy-dev] [galaxy-user] Blast2GO local instance Re: Table with gene count reads

2012-04-03 Thread Greg Von Kuster

On Apr 3, 2012, at 6:07 AM, Peter Cock wrote:

 On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster g...@bx.psu.edu wrote:
 
 On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:
 
 Have you seen the README file that comes with the
 Blast2GO wrapper? Perhaps the 'install from toolshed'
 could be tweaked to make this kind of documentation
 more visible...
 
 If you are installing a single repository that contains a file named one of
 (case is ignored) readme, readme.txt, read_me, read_me.txt, the contents of
 the file will be displayed on the tool panel section selection page.  An
 example using the antismash repository on the main tool shed is below.  This
 new feature is available in change set revision 6945:5ea04ccb61e8, which is
 currently running on the Galaxy tool shed and our central development
 repository.  It will be available in the next Galaxy distribution.
 
 Great. In this case I've actually called the file blast2go.txt (to match
 the use of blast2go.xml and blast2go.py). I didn't want to use a
 generic name like README since there could be other tools
 installed in the same folder (this predates the auto-install system).
 Is this naming pattern common used enough to justify including in
 the Galaxy Tool Shed code for spotting a README file?


Since the read me file contains instructions for installing the tools in the 
repository, would it be better to assume only 1 installation file that includes 
different instructions per contained tool if necessary?  If multiple read me 
files are allowed per repository, they would all have to be merged together 
with the entire content displayed on the tool panel section selection screen 
anyway, so allowing only a single file would be better.  The read me in your 
blast2go repository is named blast2go.txt, so I suppose we could expand the 
read me file name list to include repository name.txt.  I'll do this.


 
 Care must be taken when following instructions in README files since some of
 the information may be outdated.  For example, the Galaxy functional test
 framework was recently enhanced to support testing tools included in
 installed repositories, but I've seen some README files currently in
 repositories that instruct installers to move test data to the Galaxy
 installation environment, which is no longer necessary.
 
 Some of my tools' README files will need a little clarification following
 those changes to Galaxy.


My next big feature will be supporting installation of tool dependencies 
automatically with the repository contents, so keep that in mind if you're 
making changes to install instructions.  This enhancement will take a bit of 
time.


 
 Thanks,
 
 Peter
 


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Re: [galaxy-dev] [galaxy-user] Blast2GO local instance Re: Table with gene count reads

2012-04-02 Thread Greg Von Kuster

On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:

 
 Have you seen the README file that comes with the
 Blast2GO wrapper? Perhaps the 'install from toolshed'
 could be tweaked to make this kind of documentation
 more visible...
 


If you are installing a single repository that contains a file named one of 
(case is ignored) readme, readme.txt, read_me, read_me.txt, the contents of the 
file will be displayed on the tool panel section selection page.  An example 
using the antismash repository on the main tool shed is below.  This new 
feature is available in change set revision 6945:5ea04ccb61e8, which is 
currently running on the Galaxy tool shed and our central development 
repository.  It will be available in the next Galaxy distribution.

Care must be taken when following instructions in README files since some of 
the information may be outdated.  For example, the Galaxy functional test 
framework was recently enhanced to support testing tools included in installed 
repositories, but I've seen some README files currently in repositories that 
instruct installers to move test data to the Galaxy installation environment, 
which is no longer necessary.


Installation may take a while, depending upon the size of the repository 
contents. Wait until a message is displayed in your browser after clicking the 
Install button below.

Choose the tool panel section to contain the installed tools (optional)
Shed tool configuration file:

Your Galaxy instance is configured with 1 shed tool configuration files, so 
choose one in which to configure the installed tools.
Add new tool panel section:

Add a new tool panel section to contain the installed tools (optional).
Select existing tool panel section:
ENCODE Tools
Get Data
Choose an existing section in your tool panel to contain the installed tools 
(optional).

Clicking Install without selecting a tool panel section will load the installed 
tools into the tool panel outside of any sections.
Repository README file (may contain important installation or license 
information)
Galaxy wrapper for AntiSmash
=

This wrapper is copyright 2012 by BjXXrn GrXXning.

This is a wrapper for the command line tool of antiSMASH.

antiSMASH allows the rapid genome-wide identification, annotation and analysis 
of secondary metabolite biosynthesis gene clusters in bacterial and fungal 
genomes.
It integrates and cross-links with a large number of in silico secondary 
metabolite analysis tools.

http://antismash.secondarymetabolites.org/

Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr 
Zakrzewski, Michael A. Fischbach, Tilmann Weber, Rainer Breitling  Eriko 
Takano (2011).
antiSMASH: Rapid identification, annotation and analysis of secondary 
metabolite biosynthesis gene clusters. Nucleic Acids Research 39: W339-W346.


Installation


Currently these wrapper is tested with version 1.1 and the modified version of 
antismash.py included in that repository.

Install or downlaod antiSMASH from:

http://antismash.secondarymetabolites.org/download.html

... and follow the instructions.
Please replace the antismash.py file with the one inlcuded in that repository.
Edit the following lines in multi_antiSMASH_wrapper.py and antiSMASH_wrapper.py 
and adopt it to your installation.

blastdbpath = '/home/galaxy/bin/antismash-1.1.0/db'
pfamdbpath = '/home/galaxy/bin/antismash-1.1.0/db'
antismash_path = '/home/galaxy/bin/antismash-1.1.0/antismash.py'


To install the wrapper copy the antiSMASH folder in the galaxy tools
folder and modify the tools_conf.xml file to make the tool available to Galaxy.
For example:

section name=PKS-NRPS prediction id=pks-nrps_prediction
tool file=pks-nrps/tools/antiSMASH/antiSMASH.xml /
tool file=pks-nrps/tools/antiSMASH/multi_antiSMASH.xml /
/section


History
===

v0.1 - Initial public release


Wrapper Licence (MIT/BSD style)
===

Permission to use, copy, modify, and distribute this software and its
documentation with or without modifications and for any purpose and
without fee is hereby granted, provided that any copyright notices
appear in all copies and that both those copyright notices and this
permission notice appear in supporting documentation, and that the
names of the contributors or copyright holders not be used in
advertising or publicity pertaining to distribution of the software
without specific prior permission.

THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
OR PERFORMANCE OF THIS SOFTWARE.




Re: [galaxy-dev] [galaxy-user] Blast2GO local instance Re: Table with gene count reads

2012-03-24 Thread Peter Cock
On Fri, Mar 23, 2012 at 10:45 PM, Luciano Cosme cosme.sim...@gmail.com wrote:
 Howdy,
    Thanks Jen, I will try it tomorrow.

    I installed Blast2Go from the Toolshed in my local instance of Galaxy and
 when I try to run it I get the following error:

 Index file named 'blast2go.loc' is required by tool but not available.

    I logged as admin and the installation did not gave me any error. From
 the terminal:

 galaxy.util.shed_util DEBUG 2012-03-23 17:23:37,088 Installing repository
 'blast2go'
 galaxy.util.shed_util DEBUG 2012-03-23 17:23:37,088 Cloning
 http://testtoolshed.g2.bx.psu.edu/repos/peterjc/blast2go
 destination directory: blast2go
 requesting all changes
 adding changesets
 adding manifests
 adding file changes
 added 2 changesets with 6 changes to 3 files
 updating to branch default
 3 files updated, 0 files merged, 0 files removed, 0 files unresolved
 galaxy.util.shed_util DEBUG 2012-03-23 17:23:42,798 Updating cloned
 repository to revision 7b53cc52e7ed


    Anyway, I was thinking to use it because most of my differentially
 expressed genes are unknown. I was thinking to use Blast2GO to get them at
 least clustered in functional groups. I am not sure if that would be the
 best approach to find what might be the function of these genes. I also
 checked the list of public services that might have this tool, and Berkeley
 BOP is listed, but it seems that they no longer have the server or it was
 down when I checked (or the link is broken http://galaxy.berkeleybop.org/).


 Thank you.

 Luciano

Hi Luciano

The Galaxy team normal direct questions about local Galaxy
installs to the galaxy-dev mailing list (CC'd).

Have you seen the README file that comes with the
Blast2GO wrapper? Perhaps the 'install from toolshed'
could be tweaked to make this kind of documentation
more visible...

In order to use the Blast2GO wrapper in Galaxy you must
first install b2g4pipe (Blast2GO for pipelines) and create
your own blast2go.loc based on the blast2go.loc.sample
given. You will probably also want to install a local Blast2GO
database. None of that can be automated at the moment.

The blast2go.loc file is a list of Blast2GO profiles, which
can be used to set configuration options like weights and
thresholds. The primary use is to set the database, so
you can have an entry for the public database in Spain,
or an entry for a local database which would be MUCH
faster.

For example, locally we have Blast2GO in our Galaxy
with three databases right now - our local one which
is fast, and the recent and latest public databases
in Spain (which are comparatively slow because of
all the network access required).

Peter

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