[galaxy-dev] How to specify the availability zone when using cloudman?

[Carlos Borroto]

Hi,

I'm getting this error when trying to restart a previously used cluster:
"InvalidVolume.ZoneMismatchThe volume '' is not in the same
availability zone as instance"

I did a search and I could only find this previous email in galaxy-user:
http://lists.bx.psu.edu/pipermail/galaxy-user/2012-January/003946.html

Which while confirming I should make sure to match the new instance
zone with previous volumes zone, it does not say how to do it.

Thanks,
Carlos
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Re: [galaxy-dev] Configurable toolshed package installation to support tool-dependency-resolver-plugins

[Guest, Simon]

At Mon, 14 Oct 2013 20:22:06 -0500,
John Chilton wrote:
> 
> Simon,
> 
>   Very cool! I have two concerns. Rather than adding a new
> configuration option I think I would prefer to just check the
> configured dependency resolvers and then infer from them if the tool
> shed will be used. The configuration option strikes me as having to
> configure the same thing twice, and this change would make your setup
> slightly easier. Do you have any objection to me reworking your patch
> to do this? On the other hand, perhaps it is made more clear to the
> deployer that they are definitely disabling tool dependency
> installations if they have to add the explicit option this way.

Hi John,

I have no problem with you reworking it in that way.  There are two reasons
I didn't do that myself:

1. I would have had to change the interface to the dependency
   resolvers somehow to support this query, and I wasn't sure that was
   a good thing.

2. I wanted to make it explicit that toolshed package installation was
   disabled in this case, as I thought that would make it more likely
   this change gets accepted into the mainline.

Whichever way you Greg and Dave are happy with is OK by me.
Actually, I like your implicit approach better, so hope that's the one
that gets agreed.

cheers,
Simon
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Re: [galaxy-dev] Configurable toolshed package installation to support tool-dependency-resolver-plugins

[John Chilton]

Simon,

  Very cool! I have two concerns. Rather than adding a new
configuration option I think I would prefer to just check the
configured dependency resolvers and then infer from them if the tool
shed will be used. The configuration option strikes me as having to
configure the same thing twice, and this change would make your setup
slightly easier. Do you have any objection to me reworking your patch
to do this? On the other hand, perhaps it is made more clear to the
deployer that they are definitely disabling tool dependency
installations if they have to add the explicit option this way.

  Greg, Dave have you looked at this? In particular, do you think
there are any downsides to marking a ToolDependency as installed if
nothing has actually been installed by Galaxy? Would it be better to
add new option - EXTERNALLY_CONFIGURED?

-John

P.S. I know I said I would merge that module stuff last week, but
usegalaxy.org is running off of galaxy-central right now and I am
being extra cautious about not breaking galaxy. It will get merged
though!


On Thu, Oct 10, 2013 at 7:55 PM, Guest, Simon
 wrote:
> At Fri, 4 Oct 2013 23:12:01 -0500,
> John Chilton wrote:
>>   I understand the desire to not want to try to execute the tool shed
>> actions if tool_shed_packages are not specified in the dependency
>> resolvers list. I have created a Trello card for it
>> (https://trello.com/c/CPeU3VlR). It sounds like the new status quo
>> will be functional it will just be kind of annoying to have those
>> actions try and fail and then marked as errors, right? If that is
>> right then for this reason I don't think implementing this behavior
>> will be a high priority for the team, but if you send another
>> brilliant patch or pull request I will be happy to test it and merge
>> it.
>
> Hi John,
>
> I have now implemented this.  Mercurial changeset attached.
>
> This adds another configuration item for universe_wsgi.ini as
> documented in the updated universe_wsgi.ini.sample:
>
> # This option may be used to disable installation of package
> # dependencies from tool sheds, which usually means downloading a
> # source tarball and compiling it locally.  You would disable this if
> # you want to make use of system installed packages for example.  In
> # that case, alternative tool dependency resolvers should be
> # configured in dependency_resolvers_conf.xml
> #enable_tool_shed_package_dependency_installation = True
>
> The default behaviour is per standard toolshed.  If configured to
> False, then the package components of tool dependencies will never be
> installed from the toolshed.  Rather, they will rely on the tool
> dependency manager to resolve the requirement.  This is integrated
> with the missing_tool_dependencies status, so that if dependency
> resolution fails, the repository gets flagged with "missing tool
> dependencies" on the installed tool shed repositories page, and the
> paster.log file contains a warning of exactly what wasn't found.  Of
> course, if the dependency can be satisfied, then it's green lights all
> the way, and everything should work fine.
>
> I've tested this interactively by installing the standard emboss_5
> repository, with various combinations of environment module available
> and not.  It looks to work fine.  I'm afraid I haven't yet read up on
> the Galaxy unit testing framework, so no unit tests for now.
>
> What do you think?
>
> cheers,
> Simon
>
> ===
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> is addressed and may contain confidential and/or privileged material. Any 
> review, retransmission, dissemination or other use of, or taking of any 
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Re: [galaxy-dev] Fastx toolkit broken pipe

[UMD Bioinformatics]

On Oct 14, 2013, at 9:16 PM, Brad Chapman  wrote:

> 
> Ian;
> 
>> I have my PATH set as well as the env.sh and my ./bash_profile. Again
>> this all works fine from the command line. I don't know where else
>> Galaxy is trying to find the fastx commands.
> 
> I know zero about setting up fastx_toolkit from the toolshed but from
> reading your error messages:
> 
>> command not found cat: stdout: Broken pipe
>> command not found gzip: stdout: Broken pipe/
> 
> It looks like it's not having trouble finding fastx_toolkit, but rather
> standard unix commands 'cat' and 'gzip'. Is it possible the PATH you're
> feeding to Galaxy somehow avoids include `/bin` and `/usr/bin` (or
> wherever cat and gzip are on your system)?

This is what I have for cat and gzip

$ which cat
/bin/cat
$ which gzip
/usr/bin/gzip
$ echo $PATH
/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:

>From what i can tell they should be available on the $PATH so I'm not quite 
>sure why Galaxy cannot "see" them. 

Ian

> 
> Brad


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Re: [galaxy-dev] Fastx toolkit broken pipe

[Brad Chapman]

Ian;

> I have my PATH set as well as the env.sh and my ./bash_profile. Again
> this all works fine from the command line. I don't know where else
> Galaxy is trying to find the fastx commands.

I know zero about setting up fastx_toolkit from the toolshed but from
reading your error messages:

> command not found cat: stdout: Broken pipe
> command not found gzip: stdout: Broken pipe/

It looks like it's not having trouble finding fastx_toolkit, but rather
standard unix commands 'cat' and 'gzip'. Is it possible the PATH you're
feeding to Galaxy somehow avoids include `/bin` and `/usr/bin` (or
wherever cat and gzip are on your system)?

Brad
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Re: [galaxy-dev] Fastx toolkit broken pipe

[UMD Bioinformatics]

Hello Dave,

Here is the full log info for the failed fastx runs

galaxy.jobs.runners.local DEBUG 2013-10-14 14:24:32,512 (306) executing: cat 
'/Volumes/Jose-Drobo/WholeGenomeSequencingDataOfInterest/Ruvkun_mut16_smallRNAs/SRR087428/SRR087428.fastq'
 | fastx_reverse_complement  -Q 64  -v -o 
'/Volumes/Jose-Drobo/galaxy-dist/database/files/000/dataset_313.dat'
galaxy.jobs DEBUG 2013-10-14 14:24:32,581 (306) Persisting job destination 
(destination id: local:///)
galaxy.jobs.runners.local DEBUG 2013-10-14 14:24:32,722 execution finished: cat 
'/Volumes/Jose-Drobo/WholeGenomeSequencingDataOfInterest/Ruvkun_mut16_smallRNAs/SRR087428/SRR087428.fastq'
 | fastx_reverse_complement  -Q 64  -v -o 
'/Volumes/Jose-Drobo/galaxy-dist/database/files/000/dataset_313.dat'
galaxy.jobs.runners DEBUG 2013-10-14 14:24:32,866 executing external set_meta 
script for job 306: /Volumes/Jose-Drobo/galaxy-dist/set_metadata.sh 
./database/files 
/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306 . 
/Volumes/Jose-Drobo/galaxy-dist/universe_wsgi.ini 
/Volumes/Jose-Drobo/galaxy-dist/database/tmp/tmprYzdng 
/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/galaxy.json
 
/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_in_HistoryDatasetAssociation_312_XtTL8q,/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_kwds_HistoryDatasetAssociation_312_3MJoHa,/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_out_HistoryDatasetAssociation_312_82_iZG,/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_results_HistoryDatasetAssociation_312_k5blD2,,/Volumes/Jose-Drobo/galaxy-dist/database/job_working_directory/000/306/metadata_override_HistoryDatasetAssociation_312_tFX5kW
galaxy.jobs.runners DEBUG 2013-10-14 14:24:35,692 execution of external 
set_meta for job 306 finished
galaxy.jobs DEBUG 2013-10-14 14:24:35,781 setting dataset state to ERROR
galaxy.jobs DEBUG 2013-10-14 14:24:35,949 job 306 ended

Cheers
Ian
On Oct 14, 2013, at 12:05 PM, Dave Bouvier  wrote:

> Ian,
> 
> Although the fastx tools have been migrated to the tool shed, this migration 
> has not yet been released to the stable branch, but is planned to be included 
> in the upcoming release. In the meantime, I would suggest maintaining the 
> binary installation of the fastx dependencies using one of the options 
> described on this page:
> 
> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
> 
> After the release, you can then run the automated process to install the 
> migrated tools from the tool shed as described here:
> 
> http://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
> 
>   --Dave B.
> 
> On 10/14/2013 09:14 AM, UMD Bioinformatics wrote:
>> Dave,
>> 
>> Here is my information on the revision.
>> 
>> $ hg heads | more
>> changeset:   10421:a477486bf18e
>> branch:  stable
>> tag: tip
>> user:Nate Coraor 
>> date:Thu Sep 26 11:02:58 2013 -0400
>> summary: Bugfix for tool-to-destination mapping, tool ids are lowercased 
>> but the mapping id was not lowercased.
>> 
>> changeset:   10411:c42567f43aa7
>> user:greg
>> date:Mon Aug 19 13:19:56 2013 -0400
>> summary: Filter invalid objects when generating the list of 
>> repository_dependencies objects that are associated with a tool shed 
>> repository installed into Galaxy.
>> 
>> On Oct 14, 2013, at 9:11 AM, Dave Bouvier  wrote:
>> 
>>> Ian,
>>> 
>>> To help track down this issue, could you provide the revision of Galaxy 
>>> you're running?
>>> 
>>>   --Dave B.
>>> 
>>> On 10/14/2013 08:09 AM, UMD Bioinformatics wrote:
 Hello all,
 
 I'm still dealing with an error regarding Fastx toolkit. I all of the
 fastx commands in my /usr/local and I have installed fastx via the
 toolshed. I'm am still receiving the following error. Any help would be
 great.
 
 Cheers
 Ian
 
 An error occurred with this dataset://bin/sh: fasta_formatter: command
 not found cat: stdout: Broken pipe/
 /
 /
 /
 /
 On Oct 11, 2013, at 9:24 AM, UMD Bioinformatics
 mailto:bioinformatics@gmail.com>> wrote:
 
> Bjöern,
> 
> Here is the error message.
> 
> An error occurred with this dataset://bin/sh: fastq_to_fasta: command
> not found gzip: stdout: Broken pipe/
> /
> /
> /
> /
> On Oct 10, 2013, at 7:06 PM, Björn Grüning
>  > wrote:
> 
>> Hi Ian,
>> 
>> what mean broken pipe error, can you post the error message here?
>> 
>> Thanks,
>> Bjoern
>> 
>>> Hello,
>>> 
>>> I've got a local install of galaxy with fastx tools installed. I'm
>>> getting a broken pipe error but I'm not sure why. I install fastx
>>> using the compiler outside galaxy and it was working fine inside
>>> galaxy previously. Fas

[galaxy-dev] Consistently denied server access

[Rhea Datta]

Hello,

My account is under rrdatta@gmail.com.

I have been able to successfully transfer files and performed FTP uploads
using Filezilla in the past. However in the last few days I have been
consistently denied server access. The report I get is:

Status: Connection attempt failed with "ECONNREFUSED - Connection refused
by server".

Please let me know if you have a solution to this problem.
Thank you so much
Rhea


-- 
*Rhea R Datta, PhD*
Postdoctoral Associate
New York University
r...@nyu.edu
rrdatta@gmail.com
(917) 613 4719
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Re: [galaxy-dev] Fastx toolkit broken pipe

[UMD Bioinformatics]

Dave,

Thanks for the information. I've added the bin folder to the fastx_toolkit as 
described in the document. I also copied the executables from /usr/local/bin 
for fastx_toolkit to the devteam/backage_fastx_toolkit/0_0_13/ec66ae4c269b/bin 
as described. I've restarted Galaxy but I'm still getting an error.  My PATH 
has both /usr/local/bin and the devfolder in therm. I'm not sure why this won't 
work. 

error
An error occurred with this dataset:/bin/sh: fastq_quality_trimmer: command not 
found cat: stdout: Broken pipe

I have my PATH set as well as the env.sh and my ./bash_profile. Again this all 
works fine from the command line. I don't know where else Galaxy is trying to 
find the fastx commands. This is very frustrating.

Cheers
Ian

On Oct 14, 2013, at 12:05 PM, Dave Bouvier  wrote:

> Ian,
> 
> Although the fastx tools have been migrated to the tool shed, this migration 
> has not yet been released to the stable branch, but is planned to be included 
> in the upcoming release. In the meantime, I would suggest maintaining the 
> binary installation of the fastx dependencies using one of the options 
> described on this page:
> 
> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
> 
> After the release, you can then run the automated process to install the 
> migrated tools from the tool shed as described here:
> 
> http://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
> 
>   --Dave B.
> 
> On 10/14/2013 09:14 AM, UMD Bioinformatics wrote:
>> Dave,
>> 
>> Here is my information on the revision.
>> 
>> $ hg heads | more
>> changeset:   10421:a477486bf18e
>> branch:  stable
>> tag: tip
>> user:Nate Coraor 
>> date:Thu Sep 26 11:02:58 2013 -0400
>> summary: Bugfix for tool-to-destination mapping, tool ids are lowercased 
>> but the mapping id was not lowercased.
>> 
>> changeset:   10411:c42567f43aa7
>> user:greg
>> date:Mon Aug 19 13:19:56 2013 -0400
>> summary: Filter invalid objects when generating the list of 
>> repository_dependencies objects that are associated with a tool shed 
>> repository installed into Galaxy.
>> 
>> On Oct 14, 2013, at 9:11 AM, Dave Bouvier  wrote:
>> 
>>> Ian,
>>> 
>>> To help track down this issue, could you provide the revision of Galaxy 
>>> you're running?
>>> 
>>>   --Dave B.
>>> 
>>> On 10/14/2013 08:09 AM, UMD Bioinformatics wrote:
 Hello all,
 
 I'm still dealing with an error regarding Fastx toolkit. I all of the
 fastx commands in my /usr/local and I have installed fastx via the
 toolshed. I'm am still receiving the following error. Any help would be
 great.
 
 Cheers
 Ian
 
 An error occurred with this dataset://bin/sh: fasta_formatter: command
 not found cat: stdout: Broken pipe/
 /
 /
 /
 /
 On Oct 11, 2013, at 9:24 AM, UMD Bioinformatics
 mailto:bioinformatics@gmail.com>> wrote:
 
> Bjöern,
> 
> Here is the error message.
> 
> An error occurred with this dataset://bin/sh: fastq_to_fasta: command
> not found gzip: stdout: Broken pipe/
> /
> /
> /
> /
> On Oct 10, 2013, at 7:06 PM, Björn Grüning
>  > wrote:
> 
>> Hi Ian,
>> 
>> what mean broken pipe error, can you post the error message here?
>> 
>> Thanks,
>> Bjoern
>> 
>>> Hello,
>>> 
>>> I've got a local install of galaxy with fastx tools installed. I'm
>>> getting a broken pipe error but I'm not sure why. I install fastx
>>> using the compiler outside galaxy and it was working fine inside
>>> galaxy previously. Fastx works fine via the command line. I've
>>> checked the xml files and I don't see how galaxy cannot find the
>>> commands. I am running this off and external volume, but I don't
>>> think that matters.
>>> 
>>> Cheers
>>> Ian
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ___
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>>> http://galaxyproject.org/search/mailinglists/
>> 
>> 
>> 
>> ___
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> 
 
 
 
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Re: [galaxy-dev] Getting bowtie2 and tophat2 to work on galaxy on amazon aws cloud

[Stanislas Werfel]

Thanks.
I tried both File1 and 2 of SRR618542. Here's one of the links:
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR618/SRR618542/SRR618542_1.fastq.gz


On Oct 14, 2013, at 8:01 PM, Vipin TS wrote:

> 
> - bowtie2 does not show any built-in reference genomes
> 
> 
> by default Cloudman didn't ship the genome index for bowtie2. Bowtie2 use its 
> own index set.
> Usage: bowtie2-build [option] genome.fa index_basename
> 
> and add the entries in "bowtie2_indices.loc". Please make sure that the 
> fields are tab delimited, 
> not space delimited, and have no trailing or extra whitespace (this is easy 
> to slip in by accident).
> and place the *.loc file under /mnt/galaxyIndices/galaxy/tool-data/
> 
> Most of the genome reference file are located at base folder: 
> /mnt/galaxyIndices/genomes/
> 
> example: 
> /mnt/galaxyIndices/genomes/Athaliana/araTha_tair9/seq/Arabidopsis_thaliana.TAIR9.55.dna.toplevel.fa.gz
> 
>  
> - when I try to import a file from EBI-SRA (I paste the ftp address into 
> "Upload File") it's loading without stopping until the drive is full (>97 
> GB), although the file itself is only about 3GB. Is it a problem with the EBI 
> server or within galaxy?
> 
> I am not sure, can you please paste the url which points to the file.
> 
>  
> 
> Thanks for any help. 
> 
> 
> 
> On Oct 14, 2013, at 5:50 PM, Vipin TS wrote:
> 
>> Hi Stanislas, 
>> 
>> Please check the PATH variable and make sure that you can access bowtie2 
>> from command line and then restart the Galaxy service through cloudman 
>> interface. I think that should work. 
>> 
>> Vipin
>>  
>> 
>> I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman 
>> distribution (ami-118bfc78). The instatiated Galaxy however does not contain 
>> Bowtie2 and Tophat2, even after updating through the Cloudman Admin section. 
>> Although the wrappers are there in the tools directory, when I access it 
>> through ssh. I've also installed Bowtie2 manually on the server and the 
>> command bowtie2 does get recognized.
>> How cat I get these two to run on the Galaxy instance?
>> 
>> Thanks for your help.
>> Best
>> Stanislas
>> ___
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>> 
> 
> 

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Re: [galaxy-dev] Getting bowtie2 and tophat2 to work on galaxy on amazon aws cloud

[Vipin TS]

> - bowtie2 does not show any built-in reference genomes
>
>
by default Cloudman didn't ship the genome index for bowtie2. Bowtie2 use
its own index set.
Usage: bowtie2-build [option] genome.fa index_basename

and add the entries in "bowtie2_indices.loc". Please make sure that the fields
are tab delimited,
not space delimited, and have no trailing or extra whitespace (this is easy
to slip in by accident).
and place the *.loc file under /mnt/galaxyIndices/galaxy/tool-data/

Most of the genome reference file are located at base folder:
/mnt/galaxyIndices/genomes/

example:
/mnt/galaxyIndices/genomes/Athaliana/araTha_tair9/seq/Arabidopsis_thaliana.TAIR9.55.dna.toplevel.fa.gz



> - when I try to import a file from EBI-SRA (I paste the ftp address into
> "Upload File") it's loading without stopping until the drive is full (>97
> GB), although the file itself is only about 3GB. Is it a problem with the
> EBI server or within galaxy?
>

I am not sure, can you please paste the url which points to the file.



>
> Thanks for any help.
>
>
>
> On Oct 14, 2013, at 5:50 PM, Vipin TS wrote:
>
> Hi
> Stanislas,
>
> Please check the PATH variable and make sure that you can access bowtie2
> from command line and then restart the Galaxy service through cloudman
> interface. I think that should work.
>
> Vipin
>
>
>>
>> I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman
>> distribution (ami-118bfc78). The instatiated Galaxy however does not
>> contain Bowtie2 and Tophat2, even after updating through the Cloudman Admin
>> section. Although the wrappers are there in the tools directory, when I
>> access it through ssh. I've also installed Bowtie2 manually on the server
>> and the command bowtie2 does get recognized.
>> How cat I get these two to run on the Galaxy instance?
>>
>> Thanks for your help.
>> Best
>> Stanislas
>> ___
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>>
>
>
>
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Re: [galaxy-dev] Getting bowtie2 and tophat2 to work on galaxy on amazon aws cloud

[Stanislas Werfel]

Thanks for the quick answer. Could access bowtie2 from command line without a 
problem. Found that I had to include a line pointing to the wrapper in 
tool_conf.xml. It wasn't there by default. 
Now two new problems:

- bowtie2 does not show any built-in reference genomes

- when I try to import a file from EBI-SRA (I paste the ftp address into 
"Upload File") it's loading without stopping until the drive is full (>97 GB), 
although the file itself is only about 3GB. Is it a problem with the EBI server 
or within galaxy?

Thanks for any help. 


On Oct 14, 2013, at 5:50 PM, Vipin TS wrote:

> Hi Stanislas, 
> 
> Please check the PATH variable and make sure that you can access bowtie2 from 
> command line and then restart the Galaxy service through cloudman interface. 
> I think that should work. 
> 
> Vipin
>  
> 
> I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman 
> distribution (ami-118bfc78). The instatiated Galaxy however does not contain 
> Bowtie2 and Tophat2, even after updating through the Cloudman Admin section. 
> Although the wrappers are there in the tools directory, when I access it 
> through ssh. I've also installed Bowtie2 manually on the server and the 
> command bowtie2 does get recognized.
> How cat I get these two to run on the Galaxy instance?
> 
> Thanks for your help.
> Best
> Stanislas
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Re: [galaxy-dev] Fastx toolkit broken pipe

[Dave Bouvier]

Ian,

Although the fastx tools have been migrated to the tool shed, this 
migration has not yet been released to the stable branch, but is planned 
to be included in the upcoming release. In the meantime, I would suggest 
maintaining the binary installation of the fastx dependencies using one 
of the options described on this page:


http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

After the release, you can then run the automated process to install the 
migrated tools from the tool shed as described here:


http://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution

   --Dave B.

On 10/14/2013 09:14 AM, UMD Bioinformatics wrote:

Dave,

Here is my information on the revision.

$ hg heads | more
changeset:   10421:a477486bf18e
branch:  stable
tag: tip
user:Nate Coraor 
date:Thu Sep 26 11:02:58 2013 -0400
summary: Bugfix for tool-to-destination mapping, tool ids are lowercased 
but the mapping id was not lowercased.

changeset:   10411:c42567f43aa7
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of 
repository_dependencies objects that are associated with a tool shed repository 
installed into Galaxy.

On Oct 14, 2013, at 9:11 AM, Dave Bouvier  wrote:


Ian,

To help track down this issue, could you provide the revision of Galaxy you're 
running?

   --Dave B.

On 10/14/2013 08:09 AM, UMD Bioinformatics wrote:

Hello all,

I'm still dealing with an error regarding Fastx toolkit. I all of the
fastx commands in my /usr/local and I have installed fastx via the
toolshed. I'm am still receiving the following error. Any help would be
great.

Cheers
Ian

An error occurred with this dataset://bin/sh: fasta_formatter: command
not found cat: stdout: Broken pipe/
/
/
/
/
On Oct 11, 2013, at 9:24 AM, UMD Bioinformatics
mailto:bioinformatics@gmail.com>> wrote:


Bjöern,

Here is the error message.

An error occurred with this dataset://bin/sh: fastq_to_fasta: command
not found gzip: stdout: Broken pipe/
/
/
/
/
On Oct 10, 2013, at 7:06 PM, Björn Grüning
mailto:bjoern.gruen...@pharmazie.uni-freiburg.de>> wrote:


Hi Ian,

what mean broken pipe error, can you post the error message here?

Thanks,
Bjoern


Hello,

I've got a local install of galaxy with fastx tools installed. I'm
getting a broken pipe error but I'm not sure why. I install fastx
using the compiler outside galaxy and it was working fine inside
galaxy previously. Fastx works fine via the command line. I've
checked the xml files and I don't see how galaxy cannot find the
commands. I am running this off and external volume, but I don't
think that matters.

Cheers
Ian





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Re: [galaxy-dev] AttributeError: type object 'InvalidJobException' has no attribute 'name'

[Nate Coraor]

On Oct 14, 2013, at 6:07 AM, Peter Cock wrote:

> On Fri, Oct 11, 2013 at 9:12 AM, Peter Cock  wrote:
>> On Thu, Oct 10, 2013 at 8:20 PM, Nate Coraor  wrote:
>>> Hi all,
>>> 
>>> The recent changes to the DRMAA runner are for better handling
>>> of job-ending conditions under slurm, but it looks like SGE has
>>> different behavior when a job finishes.  I'll provide a fix for this
>>> shortly, in the meantime, it's fine to use a slightly older version
>>> of drmaa.py.
>>> 
>>> --nate
>> 
>> Thanks Nate,
>> 
>> So far I've only seen this once so it isn't urgent for me.
>> 
>> Peter
> 
> Hi Nate,
> 
> I see you've fix the name attribute error:
> https://bitbucket.org/galaxy/galaxy-central/commits/ff76fd33b81cdde1fb270de688ec5e86488ba34d
> 
> However it seems the underlying problem (job check resulted in:
> code 18: The job specified by the 'jobid' does not exist.) is affecting
> other people now:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-October/017002.html
> 
> Peter


Hi Peter,

I'm working on refactoring the DRMAA runner to allow for these different DRM 
behaviors without duplicating the code.  In the interim, I've reverted the 
change to the DRMAA runner that resulted in the observed behavior in changeset 
d46b64f12c52.

Thanks,
--nate
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Re: [galaxy-dev] Getting bowtie2 and tophat2 to work on galaxy on amazon aws cloud

[Vipin TS]

Hi
Stanislas,

Please check the PATH variable and make sure that you can access bowtie2
from command line and then restart the Galaxy service through cloudman
interface. I think that should work.

Vipin


>
> I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman
> distribution (ami-118bfc78). The instatiated Galaxy however does not
> contain Bowtie2 and Tophat2, even after updating through the Cloudman Admin
> section. Although the wrappers are there in the tools directory, when I
> access it through ssh. I've also installed Bowtie2 manually on the server
> and the command bowtie2 does get recognized.
> How cat I get these two to run on the Galaxy instance?
>
> Thanks for your help.
> Best
> Stanislas
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[galaxy-dev] Getting bowtie2 and tophat2 to work on galaxy on amazon aws cloud

[Stanislas Werfel]

Dear all,

I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman 
distribution (ami-118bfc78). The instatiated Galaxy however does not contain 
Bowtie2 and Tophat2, even after updating through the Cloudman Admin section. 
Although the wrappers are there in the tools directory, when I access it 
through ssh. I've also installed Bowtie2 manually on the server and the command 
bowtie2 does get recognized.
How cat I get these two to run on the Galaxy instance?

Thanks for your help.
Best
Stanislas
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Re: [galaxy-dev] Problem in get_tool_shed_status_for_installed_repository()

[Greg Von Kuster]

Hello Simon,

On Oct 14, 2013, at 6:26 AM, Greg Von Kuster  wrote:

> On Oct 13, 2013, at 5:13 PM, Simon Guest  wrote:
> 
>> 
>> I've recently upgraded to the
>> development branch, and I'm getting HTTP 404 errors from the new
>> function get_tool_shed_status_for_installed_repository().
>> 
>> What gets logged is this:
>> tool_shed.util.shed_util_common ERROR 2013-10-14 09:44:17,448 Error 
>> attempting to get tool shed status for installed repository 
>> emboss_datatypes: HTTP Error 404: Not Found
>> Traceback (most recent call last):
>> File "/home/galaxy-dev/galaxy/lib/tool_shed/util/shed_util_common.py", line 
>> 1226, in get_tool_shed_status_for_installed_repository
>> encoded_tool_shed_status_dict = common_util.tool_shed_get( app, 
>> tool_shed_url, url )
>> File "/home/galaxy-dev/galaxy/lib/tool_shed/util/common_util.py", line 191, 
>> in tool_shed_get
>> response = urlopener.open( uri )
>> File "/usr/lib64/python2.6/urllib2.py", line 397, in open
>> response = meth(req, response)
>> File "/usr/lib64/python2.6/urllib2.py", line 510, in http_response
>> 'http', request, response, code, msg, hdrs)
>> File "/usr/lib64/python2.6/urllib2.py", line 435, in error
>> return self._call_chain(*args)
>> File "/usr/lib64/python2.6/urllib2.py", line 369, in _call_chain
>> result = func(*args)
>> File "/usr/lib64/python2.6/urllib2.py", line 518, in http_error_default
>> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
>> HTTPError: HTTP Error 404: Not Found
>> 
>> 


The above issue should be corrected in 10893:02b18fd5432e.


>> 
>> When's the next stable release planned to be released, and what should
>> I expect to be in it?


The latest tentative date for the next Galaxy release is November 4, and the 
contents of the release will be included in the associated Galaxy Development 
News Brief.


>> 
>> cheers,
>> Simon
>> ===
>> Attention: The information contained in this message and/or attachments from 
>> AgResearch Limited is intended only for the persons or entities to which it 
>> is addressed and may contain confidential and/or privileged material. Any 
>> review, retransmission, dissemination or other use of, or taking of any 
>> action in reliance upon, this information by persons or entities other than 
>> the intended recipients is prohibited by AgResearch Limited. If you have 
>> received this message in error, please notify the sender immediately.
>> ===
>> 
> 
> 
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Re: [galaxy-dev] Fastx toolkit broken pipe

[UMD Bioinformatics]

Dave,

Here is my information on the revision.

$ hg heads | more
changeset:   10421:a477486bf18e
branch:  stable
tag: tip
user:Nate Coraor 
date:Thu Sep 26 11:02:58 2013 -0400
summary: Bugfix for tool-to-destination mapping, tool ids are lowercased 
but the mapping id was not lowercased.

changeset:   10411:c42567f43aa7
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of 
repository_dependencies objects that are associated with a tool shed repository 
installed into Galaxy.

On Oct 14, 2013, at 9:11 AM, Dave Bouvier  wrote:

> Ian,
> 
> To help track down this issue, could you provide the revision of Galaxy 
> you're running?
> 
>   --Dave B.
> 
> On 10/14/2013 08:09 AM, UMD Bioinformatics wrote:
>> Hello all,
>> 
>> I'm still dealing with an error regarding Fastx toolkit. I all of the
>> fastx commands in my /usr/local and I have installed fastx via the
>> toolshed. I'm am still receiving the following error. Any help would be
>> great.
>> 
>> Cheers
>> Ian
>> 
>> An error occurred with this dataset://bin/sh: fasta_formatter: command
>> not found cat: stdout: Broken pipe/
>> /
>> /
>> /
>> /
>> On Oct 11, 2013, at 9:24 AM, UMD Bioinformatics
>> mailto:bioinformatics@gmail.com>> wrote:
>> 
>>> Bjöern,
>>> 
>>> Here is the error message.
>>> 
>>> An error occurred with this dataset://bin/sh: fastq_to_fasta: command
>>> not found gzip: stdout: Broken pipe/
>>> /
>>> /
>>> /
>>> /
>>> On Oct 10, 2013, at 7:06 PM, Björn Grüning
>>> >> > wrote:
>>> 
 Hi Ian,
 
 what mean broken pipe error, can you post the error message here?
 
 Thanks,
 Bjoern
 
> Hello,
> 
> I've got a local install of galaxy with fastx tools installed. I'm
> getting a broken pipe error but I'm not sure why. I install fastx
> using the compiler outside galaxy and it was working fine inside
> galaxy previously. Fastx works fine via the command line. I've
> checked the xml files and I don't see how galaxy cannot find the
> commands. I am running this off and external volume, but I don't
> think that matters.
> 
> Cheers
> Ian
> 
> 
> 
> 
> 
> ___
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>>> 
>> 
>> 
>> 
>> ___
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Re: [galaxy-dev] Fastx toolkit broken pipe

[Dave Bouvier]

Ian,

To help track down this issue, could you provide the revision of Galaxy 
you're running?


   --Dave B.

On 10/14/2013 08:09 AM, UMD Bioinformatics wrote:

Hello all,

I'm still dealing with an error regarding Fastx toolkit. I all of the
fastx commands in my /usr/local and I have installed fastx via the
toolshed. I'm am still receiving the following error. Any help would be
great.

Cheers
Ian

An error occurred with this dataset://bin/sh: fasta_formatter: command
not found cat: stdout: Broken pipe/
/
/
/
/
On Oct 11, 2013, at 9:24 AM, UMD Bioinformatics
mailto:bioinformatics@gmail.com>> wrote:


Bjöern,

Here is the error message.

An error occurred with this dataset://bin/sh: fastq_to_fasta: command
not found gzip: stdout: Broken pipe/
/
/
/
/
On Oct 10, 2013, at 7:06 PM, Björn Grüning
mailto:bjoern.gruen...@pharmazie.uni-freiburg.de>> wrote:


Hi Ian,

what mean broken pipe error, can you post the error message here?

Thanks,
Bjoern


Hello,

I've got a local install of galaxy with fastx tools installed. I'm
getting a broken pipe error but I'm not sure why. I install fastx
using the compiler outside galaxy and it was working fine inside
galaxy previously. Fastx works fine via the command line. I've
checked the xml files and I don't see how galaxy cannot find the
commands. I am running this off and external volume, but I don't
think that matters.

Cheers
Ian





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Re: [galaxy-dev] Test Toolshed Biopython package dependency & NumPy

[Dave Bouvier]

Peter,

I've made some changes to the way the test VM handles tool dependencies, 
which should reduce the frequency of this type of error, and will be 
running further tests today to see how I can improve the framework's 
handling of these situations.


   --Dave B.

On 10/11/2013 04:51 AM, Peter Cock wrote:

On Thu, Oct 10, 2013 at 10:00 AM, Peter Cock  wrote:

On Wed, Oct 9, 2013 at 10:01 PM, Björn Grüning
 wrote:

Am Mittwoch, den 09.10.2013, 19:15 +0100 schrieb Peter Cock:

On Tue, Oct 8, 2013 at 9:57 PM, Dave Bouvier  wrote:

Peter, Björn,

I have restored gfortran to the repository test host. I believe it was
inadvertently removed, possibly as a side effect of updating packages or
removing packages that were causing conflicts with the Galaxy eggs. Numpy
and biopython should now install successfully, as they do in my local
environment.

--Dave B.


Thanks Dave, fingers crossed for tonight's test run :)

Bjoern - it looks like we can leave the NumPy definition as is...


Ah sorry, totally forgot about it :(



Progress, Fortran is working and lapack seems to have installed, but:
e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename

Installation errors - no functional tests were run for any tools in
this changeset revision
Tool dependencies
TypeNameVersion
biopython package 1.62
Error
running install Numerical Python (NumPy) is not installed. This
package is required for many Biopython features. Please install it
before you install Biopython. You can install Biopython anyway, but
anything dependent on NumPy will not work. If you do this, and later
install NumPy, you should then re-install Biopython. You can find
NumPy at http://numpy.scipy.org
TypeNameVersion
numpy package 1.7.1
Error
Running from numpy source directory.
/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmp3kNwuR/tmp-toolshed-mtdGJ0d5H/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__)
/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmp3kNwuR/tmp-toolshed-mtdGJ0d5H/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__)
error: Command "/usr/bin/gfortran -Wall -Wall -shared
build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o
build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o
-L/ToolDependencies/lapack/3.4.2/iuc/package_lapack_3_4/60957bd68fe2/lapack/lib
-Lbuild/temp.linux-x86_64-2.7 -llapack -lblas -lgfortran -o
build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so" failed with
exit status 1


Most of that is warnings about not using ATLAS (which we
expect) but I'm not quite sure why it fails...


Hi Guys,

Bjoern - good news for you, the installation of NumPy can
work on the current Test Tool Shed.

Dave - bad news for you, last night I had 3 NumPy install failures
(all different) and 2 successes - which to me suggests a possible
race condition in the nightly testing?

(1) Last night on the Test Tool Shed this failed as in email above:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/834cf6618a14

(2) This failed with the simpler message:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/308ec20faefb

Installation errors - no functional tests were run for any tools in
this changeset revision
Tool dependencies
TypeNameVersion
biopython package 1.62
Error
running install Numerical Python (NumPy) is not installed. This
package is required for many Biopython features. Please install it
before you install Biopython. You can install Biopython anyway, but
anything dependent on NumPy will not work. If you do this, and later
install NumPy, you should then re-install Biopython. You can find
NumPy at http://numpy.scipy.org

(3) Here the installation seems to have failed silently, leading to a
test failure at the import stage:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/9e9e3b860aa0

Tests that failed
Tool id: seq_select_by_id
Tool version: seq_select_by_id
Test: test_tool_00
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_select_by_id/seq_select_by_id/0.0.6)
Stderr:
Fatal error: Exit code 1 ()
Biopython 1.54 or later is required

(4, 5) However these also depend on Biopython 1.62 and worked:

http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/d08767ae73ce
(failed last night)

http://testtoolshed.g2.bx.psu.edu/view/peterj

Re: [galaxy-dev] Fastx toolkit broken pipe

[UMD Bioinformatics]

Hello all,

I'm still dealing with an error regarding Fastx toolkit. I all of the fastx 
commands in my /usr/local and I have installed fastx via the toolshed. I'm am 
still receiving the following error. Any help would be great.

Cheers
Ian

An error occurred with this dataset:/bin/sh: fasta_formatter: command not found 
cat: stdout: Broken pipe


On Oct 11, 2013, at 9:24 AM, UMD Bioinformatics  
wrote:

> Bjöern,
> 
> Here is the error message. 
> 
> An error occurred with this dataset:/bin/sh: fastq_to_fasta: command not 
> found gzip: stdout: Broken pipe
> 
> 
> On Oct 10, 2013, at 7:06 PM, Björn Grüning 
>  wrote:
> 
>> Hi Ian,
>> 
>> what mean broken pipe error, can you post the error message here?
>> 
>> Thanks,
>> Bjoern
>> 
>>> Hello,
>>> 
>>> I've got a local install of galaxy with fastx tools installed. I'm getting 
>>> a broken pipe error but I'm not sure why. I install fastx using the 
>>> compiler outside galaxy and it was working fine inside galaxy previously. 
>>> Fastx works fine via the command line. I've checked the xml files and I 
>>> don't see how galaxy cannot find the commands. I am running this off and 
>>> external volume, but I don't think that matters.
>>> 
>>> Cheers
>>> Ian
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ___
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>>>  http://galaxyproject.org/search/mailinglists/
>> 
>> 
>> 
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Re: [galaxy-dev] SeqPrep wrapper?

[Lionel Guy]

Hi Brad,

(cc-ing the list)

I'm more interested in the merging part, and after a quick search on the 
toolshed, there are no tools to merge reads. Seems that there is a need for a 
read merger wrapper then...

Lionel

On 14 Oct 2013, at 13:46 , "Langhorst, Brad"  wrote:

> I would also like to see a seqprep wrapper… 
> if you need something sooner, cutdadapt is already wrapped and i'm pretty 
> sure there is an existing tool to merge reads as well.
> 
> Brad
> --
> Brad Langhorst
> Applications and Product Development Scientist
> 
> On Oct 14, 2013, at 6:59 AM, Lionel Guy 
> wrote:
> 
>> Hi,
>> 
>> I'm interested in a wrapper for SeqPrep:
>> https://github.com/jstjohn/SeqPrep
>> Anyone preparing one/aware of someone preparing one? Otherwise I'll put one 
>> together.
>> 
>> From its description: "SeqPrep is a program to merge paired end Illumina 
>> reads that are overlapping into a single longer read. It may also just be 
>> used for its adapter trimming feature without doing any paired end overlap."
>> 
>> Cheers,
>> 
>> Lionel
>> 
>> Lionel Guy
>> Uppsala University
>> ___
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> 

--
Lionel Guy 
Fålhagsleden 13, SE-75324 Uppsala | email: guy.lio...@gmail.com | mobile: +46 
(0)73 9760618 | phone: +46 (0)18 410 7398


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[galaxy-dev] SeqPrep wrapper?

[Lionel Guy]

Hi,

I'm interested in a wrapper for SeqPrep:
https://github.com/jstjohn/SeqPrep
Anyone preparing one/aware of someone preparing one? Otherwise I'll put 
one together.


From its description: "SeqPrep is a program to merge paired end 
Illumina reads that are overlapping into a single longer read. It may 
also just be used for its adapter trimming feature without doing any 
paired end overlap."


Cheers,

Lionel

Lionel Guy
Uppsala University
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Re: [galaxy-dev] Problem in get_tool_shed_status_for_installed_repository()

[Greg Von Kuster]

Hello imon,

You are correct - this feature is not yet available on the main tool shed.  
I'll add some code to handle this issue in a better way.  However, the fact 
that the main tool shed is not currently handles in a better way doesn't really 
cause any problems in this case.  So if you wanted to run the development 
branch, the current behavior for this feature should not keep you from doing so.

Thanks for reporting this.

Greg Von Kuster

On Oct 13, 2013, at 5:13 PM, Simon Guest  wrote:

> Hi Greg,
> 
> I think this would be yours.  I've recently upgraded to the
> development branch, and I'm getting HTTP 404 errors from the new
> function get_tool_shed_status_for_installed_repository().
> 
> What gets logged is this:
> tool_shed.util.shed_util_common ERROR 2013-10-14 09:44:17,448 Error 
> attempting to get tool shed status for installed repository emboss_datatypes: 
> HTTP Error 404: Not Found
> Traceback (most recent call last):
> File "/home/galaxy-dev/galaxy/lib/tool_shed/util/shed_util_common.py", line 
> 1226, in get_tool_shed_status_for_installed_repository
>  encoded_tool_shed_status_dict = common_util.tool_shed_get( app, 
> tool_shed_url, url )
> File "/home/galaxy-dev/galaxy/lib/tool_shed/util/common_util.py", line 191, 
> in tool_shed_get
>  response = urlopener.open( uri )
> File "/usr/lib64/python2.6/urllib2.py", line 397, in open
>  response = meth(req, response)
> File "/usr/lib64/python2.6/urllib2.py", line 510, in http_response
>  'http', request, response, code, msg, hdrs)
> File "/usr/lib64/python2.6/urllib2.py", line 435, in error
>  return self._call_chain(*args)
> File "/usr/lib64/python2.6/urllib2.py", line 369, in _call_chain
>  result = func(*args)
> File "/usr/lib64/python2.6/urllib2.py", line 518, in http_error_default
>  raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
> HTTPError: HTTP Error 404: Not Found
> 
> When I enhanced the log output like this:
>  log.exception( "Error attempting to get tool shed status for installed 
> repository %s (%s) (%s): %s" % ( str( repository.name ), str(tool_shed_url), 
> str(url), str( e ) ) )
> I saw this in the log:
> tool_shed.util.shed_util_common ERROR 2013-10-14 09:55:26,584 Error 
> attempting to get tool shed status for installed repository emboss_datatypes 
> (http://toolshed.g2.bx.psu.edu) 
> (http://toolshed.g2.bx.psu.edu/repository/status_for_installed_repository?name=emboss_datatypes&owner=devteam&changeset_revision=a89163f31369):
>  HTTP Error 404: Not Found
> 
> It occurs to me that the main toolshed may not be running with this
> feature enabled yet, and perhaps I should just ignore this error for
> now?  (I'd like to be running the development branch for other
> features it gives me.  Alternatively, I could think about back-porting
> the features I really need to stable, but that sounds like more work
> than I have time for.)
> 
> When's the next stable release planned to be released, and what should
> I expect to be in it?
> 
> cheers,
> Simon
> ===
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> is addressed and may contain confidential and/or privileged material. Any 
> review, retransmission, dissemination or other use of, or taking of any 
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> 


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Re: [galaxy-dev] AttributeError: type object 'InvalidJobException' has no attribute 'name'

[Peter Cock]

On Fri, Oct 11, 2013 at 9:12 AM, Peter Cock  wrote:
> On Thu, Oct 10, 2013 at 8:20 PM, Nate Coraor  wrote:
>> Hi all,
>>
>> The recent changes to the DRMAA runner are for better handling
>> of job-ending conditions under slurm, but it looks like SGE has
>> different behavior when a job finishes.  I'll provide a fix for this
>> shortly, in the meantime, it's fine to use a slightly older version
>> of drmaa.py.
>>
>> --nate
>
> Thanks Nate,
>
> So far I've only seen this once so it isn't urgent for me.
>
> Peter

Hi Nate,

I see you've fix the name attribute error:
https://bitbucket.org/galaxy/galaxy-central/commits/ff76fd33b81cdde1fb270de688ec5e86488ba34d

However it seems the underlying problem (job check resulted in:
code 18: The job specified by the 'jobid' does not exist.) is affecting
other people now:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-October/017002.html

Peter
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[galaxy-dev] jobid exception

[Rémy Dernat]

Hi,

After a big upgrade, I have an error when I submit job to SGE through drmaa

Here is the error I get:
galaxy.jobs.runners.drmaa WARNING 2013-10-14 11:26:08,075 (15615/68154) job
check resulted in InvalidJobException: code 18: The job specified by the
'jobid' does not exist.

The job is launch to sge because I see it with "qstat" SGE command. On the
galaxy Web interface, the job is stuck in yellow (running state), although
it is finished.

When I submit job by using "local" destination it works fine.


Here is my job_conf.xml file :














-q all.q -V






Any help would be usefull.

Regards,
Rem
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