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Blast2GO local instance Re: Table with gene count reads

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Blast2GO local instance Re: Table with gene count reads

Luciano Cosme
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

  

On Fri, Mar 23, 2012 at 8:43 AM, Jennifer Jackson <[hidden email]> wrote:
Hello Luciano,

There is no single tool do to this operation (although there has been some discussion about including one in the Tool Shed), but the same information can be obtained by using a combination of existing tools.

First, start by converting both starting datasets to interval format.

mapped reads:
 - for TopHat output, "NGS: SAM Tools -> Convert SAM to interval"
features:
 - for GFF file (convert to tabular if necessary), subtract "1"
   from the start position's value using tool "Text Manipulation ->
   Compute"
 - cut columns chrom, new start, stop, strand, name, and score from
   this result file using "Text Manipulation -> Cut"
 - set the data type to "interval" using the 'Edit attributes form
   (pencil icon)

Next, use a tool in the group "Operate on Genomic Intervals" to compare these intervals for overlap. The tool "Cluster" with the option "Find" is mostly likely the one you will want to use.

As a final step, summarize the data by feature using the tool "Join, Subtract and Group -> Group".

Hopefully this helps,

Best,

Jen
Galaxy team


On 3/19/12 4:36 PM, Luciano Cosme wrote:
Hi,
   I was wondering if there is any tool on Galaxy were I can obtain a
table with how many reads have been mapped to a given sample and to a
given gene (for example, use a Tophat output and use a GFF file to
obtain the table). I am using HTSeq to get it (htseq-count). There is
also GenomicRanges and easyRNASeq packages in bioconductor.
Thank you.

Luciano



___________________________________________________________
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Galaxy analysis and other features on the public server
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Re: Blast2GO local instance Re: Table with gene count reads

Peter Cock
On Fri, Mar 23, 2012 at 10:45 PM, Luciano Cosme <[hidden email]> 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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Galaxy analysis and other features on the public server
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using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
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Re: Blast2GO local instance Re: Table with gene count reads

Greg Von Kuster-2

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




___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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Re: Blast2GO local instance Re: Table with gene count reads

Peter Cock
On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster <[hidden email]> 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

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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Re: Blast2GO local instance Re: Table with gene count reads

Greg Von Kuster-2

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

> On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster <[hidden email]> 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
>


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/
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