Re: [galaxy-dev] Trimmomatic doesn't recognise pair collection

[Peter van Heusden]

Hi Peter

We found that it was a problem in the Galaxy code - it was fixed in the
some of the patches that went towards the 16.01 release.

Thanks,
Peter


On 4 February 2016 at 13:47, Peter Briggs 
wrote:

> Hello Peter
>
> I'm the author of the Trimmomatic tool on the toolshed (i.e.
> https://toolshed.g2.bx.psu.edu/view/pjbriggs/trimmomatic) - apologies for
> not responding sooner.
>
> The tool works for me on our production server (v15.10 from github) when
> using a pair of fastqs as input, by which I mean that it allows me to
> select a fastq-pair dataset as input and produces 2 fastq-pair datasets.
> (I'm haven't tried on a list of pairs.)
>
> What do you see when you say that the tool 'is not working'? I'm wondering
> if it is a problem with the tool itself, or something to do with the
> underlying Galaxy infrastructure when using the head of the dev branch).
>
> Best wishes
>
> Peter
>
>
> On 22/01/16 13:53, Peter van Heusden wrote:
>
>> Hi there
>>
>> I've got Trimmomatic installed (from the toolshed) into our local Galaxy
>> server (server is latest commit on the dev branch from GitHub). It
>> refuses to see a dataset pair as a valid input, however.
>>
>> I've tested this with two types: firstly a pair made out of 2 individual
>> datasets (both fastqsanger) and then also a list of pairs. I've tested
>> this with 'planemo serve' and the tool works, but for some reason it is
>> not working on our server. Any ideas?
>>
>> Thanks,
>> Peter
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>http://galaxyproject.org/search/mailinglists/
>>
>>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] planemo reports test failure when test succeeds

[Peter van Heusden]

Zipho looked at this over here and had some ideas about how some warning
output might trigger this spurious failure - I haven't had time to follow
up on that theory.

On 4 February 2016 at 14:26, Peter Briggs 
wrote:

> Hello again Peter
>
> I also see this when using planemo to run the tool tests both on
> trimmomatic and also on another of our tools i.e. one or more of the tests
> will be reported as 'failed' on the command line when the HTML report
> indicates that all tests executed successfully.
>
> Now I think about it, planemo itself must exit with status 0 in these
> cases as my tests on Travis-CI also report success, for example see:
>
> https://travis-ci.org/fls-bioinformatics-core/galaxy-tools/jobs/104643315
>
> Scroll to the bottom of the log and the last test is reported as 'failed',
> however the Travis test overall passes. I hadn't really thought about it
> before since the planemo exit status seems to be correct (i.e. in cases
> where there are genuine tool test failures, it will return a non-zero
> status at the end which causes Travis to correctly report a failure).
>
> (Btw this referenced above used planemo 0.22.2 but I've seen it in older
> versions too.)
>
> I don't think I've ever seen planemo report a 'passed' test as 'failed',
> but generally I check the HTML to verify whether the failures are real or
> not.
>
> Best wishes
>
> Peter
>
>
> On 22/01/16 11:40, Peter van Heusden wrote:
>
>> Hi there
>>
>> When testing the latest trimmomatic tool (from
>>
>> https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmomatic
>> ,
>> planemo test reports an error on the last test, but according to the
>> test report the test has succeeded (see attached HTML and JSON). For the
>> test setup you need to set some environment variables:
>>
>> TRIMMOMATIC_DIR - the location of the trimmomatic jar
>> TRIMMOMATIC_JAR - the name of the jar file
>> TRIMMOMATIC_ADAPTERS_DIR - location of adapters
>>
>> This is with planemo 0.22.2 and a fresh $HOME/.planemo.
>>
>> Any ideas?
>>
>> Peter
>>
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>http://galaxyproject.org/search/mailinglists/
>>
>>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Trimmomatic doesn't recognise pair collection

[Peter Briggs]

Hello Peter

Glad that you found the problem, thanks for the update.

Best wishes

Peter

On 04/02/16 12:20, Peter van Heusden wrote:

Hi Peter

We found that it was a problem in the Galaxy code - it was fixed in the
some of the patches that went towards the 16.01 release.

Thanks,
Peter


On 4 February 2016 at 13:47, Peter Briggs > wrote:

Hello Peter

I'm the author of the Trimmomatic tool on the toolshed (i.e.
https://toolshed.g2.bx.psu.edu/view/pjbriggs/trimmomatic) -
apologies for not responding sooner.

The tool works for me on our production server (v15.10 from github)
when using a pair of fastqs as input, by which I mean that it allows
me to select a fastq-pair dataset as input and produces 2 fastq-pair
datasets. (I'm haven't tried on a list of pairs.)

What do you see when you say that the tool 'is not working'? I'm
wondering if it is a problem with the tool itself, or something to
do with the underlying Galaxy infrastructure when using the head of
the dev branch).

Best wishes

Peter


On 22/01/16 13:53, Peter van Heusden wrote:

Hi there

I've got Trimmomatic installed (from the toolshed) into our
local Galaxy
server (server is latest commit on the dev branch from GitHub). It
refuses to see a dataset pair as a valid input, however.

I've tested this with two types: firstly a pair made out of 2
individual
datasets (both fastqsanger) and then also a list of pairs. I've
tested
this with 'planemo serve' and the tool works, but for some
reason it is
not working on our server. Any ideas?

Thanks,
Peter


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/


--
Peter Briggs peter.bri...@manchester.ac.uk

Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/




___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/



--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Galaxy sending jobs to multiple clusters

[Nikolay Aleksandrov Vazov]

Thank you , Nate,


Then, to be on the safe side,  the recipe will be  (including multicluster 
support):


ON SUBMIT HOST:

1) Pull Nate's version of slurm-drmaa and compile

2) Recompile Slurm client using your patch (on the submit hosts) and use it 
instead the old one containing the unmodified libslurmdb.so


No changes to Slurm on the controllers is needed


Thank you very much again !!


PS :) I'll have to merge your slurm-drmaa and mine, I have also ripped it off a 
bit :):)


Best regards


Nikolay



===
Nikolay Vazov, PhD
Department for Research Computing, University of Oslo

From: Nate Coraor 
Sent: 03 February 2016 22:19
To: Nikolay Aleksandrov Vazov
Cc: Ganote, Carrie L; John Chilton; dannon.ba...@gmail.com; 
galaxy-dev@lists.galaxyproject.org
Subject: Re: Galaxy sending jobs to multiple clusters

On Wed, Feb 3, 2016 at 10:09 AM, Nikolay Aleksandrov Vazov 
> wrote:

​Hi, Nate,


Yes, we are using slurmdbd here. So by controllers, if I get it right,  you 
mean the controller machines of each cluster which shall connect to (share) the 
same slurmdbd.

Correct.



And a last one :


In your github version you say about using Slurm >= 14.11. We are running Slurm 
14.03 and we shall have to recompile it. Do you mean by recompilation that we 
have to recompile both server Slurm part and the client Slurm on the submit 
hosts.

This is a bit tricky. If you don't need to specify multiple clusters when 
submitting (e.g. with `--clusters=cluster1,cluster2`) then it works like this:

You will need to recompile Slurm with the patch shown on Github. You don't 
actually have to install this recompiled version if you don't want to, you only 
need to make sure that slurm-drmaa uses this recompiled version's libslurmdb.so 
at runtime. There are a variety of ways to do this, I list a couple in the 
instructions. Or if you don't mind using this modified version in place of your 
existing version, you can just install the modified version so that the 
"default" libslurmdb.so is compatible. In that case, no runtime linker tricks 
should be necessary. You do not have to compile slurm-drmaa against the 
modified version.

If you *do* need multicluster submission support, you have to compile 
slurm-drmaa against a copy of the (unmodified) Slurm source code for access to 
the private headers contained within. Once done, it works the same as above - 
you still need to compile a modified libslurmdb.so. The version of 
libslurmdb.so used by slurm-drmaa at runtime is the key.

In both cases, this only needs to be done on the submission host. No 
(controller) server modifications are necessary.



Best regards


Nikolay


===
Nikolay Vazov, PhD
Department for Research Computing, University of Oslo

From: Nate Coraor >
Sent: 03 February 2016 15:56
To: Nikolay Aleksandrov Vazov
Cc: Ganote, Carrie L; John Chilton; 
dannon.ba...@gmail.com; 
galaxy-dev@lists.galaxyproject.org

Subject: Re: Galaxy sending jobs to multiple clusters

On Tue, Feb 2, 2016 at 9:18 AM, Nikolay Aleksandrov Vazov 
> wrote:


Many thanks to all of you!!



Definitely Nate's approach is a better choice. We are running Slurm 14.03, but 
Nate's manual is exhaustive enough to recompile even the existing version. (I 
don't know how we can do this on a running cluster though :) I will most 
probably go for this solution.


There is a sentence in Nate's answer  I don't really understand :


"... using `--clusters` means you have to have your controllers integrated 
using slurmdbd, ..."


what do you mean by this, Nate?

You have to run slurmdbd (it's optional) and your slurm controllers must 
connect to a single slurmdbd instance. This is Slurm's accounting server. 
Here's the documentation:

http://slurm.schedmd.com/accounting.html

The setup is relatively simple, you just need to have a MySQL (or derivative) 
server for it to store records in.

--nate





Carie, I don't actually get how you implemented the hack : did you reduplicate 
the


class DRMAAJobRunner


under a different name in drmaa.py? And where do you define every next cluster 
(controller machines)?


Can you give me some more detalis?


Thank you


Nikolay





===
Nikolay Vazov, PhD
Department for Research Computing, University of Oslo

From: Nate Coraor >
Sent: 01 February 2016 17:28
To: Ganote, Carrie L
Cc: John Chilton; Nikolay Aleksandrov Vazov; 
dannon.ba...@gmail.com; 
galaxy-dev@lists.galaxyproject.org

Subject: Re: Galaxy sending jobs to multiple clusters

Hi Nikolay,

It's worth noting that using 

Re: [galaxy-dev] planemo reports test failure when test succeeds

[Peter Briggs]

Hello again Peter

I also see this when using planemo to run the tool tests both on 
trimmomatic and also on another of our tools i.e. one or more of the 
tests will be reported as 'failed' on the command line when the HTML 
report indicates that all tests executed successfully.


Now I think about it, planemo itself must exit with status 0 in these 
cases as my tests on Travis-CI also report success, for example see:


https://travis-ci.org/fls-bioinformatics-core/galaxy-tools/jobs/104643315

Scroll to the bottom of the log and the last test is reported as 
'failed', however the Travis test overall passes. I hadn't really 
thought about it before since the planemo exit status seems to be 
correct (i.e. in cases where there are genuine tool test failures, it 
will return a non-zero status at the end which causes Travis to 
correctly report a failure).


(Btw this referenced above used planemo 0.22.2 but I've seen it in older 
versions too.)


I don't think I've ever seen planemo report a 'passed' test as 'failed', 
but generally I check the HTML to verify whether the failures are real 
or not.


Best wishes

Peter

On 22/01/16 11:40, Peter van Heusden wrote:

Hi there

When testing the latest trimmomatic tool (from
https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmomatic,
planemo test reports an error on the last test, but according to the
test report the test has succeeded (see attached HTML and JSON). For the
test setup you need to set some environment variables:

TRIMMOMATIC_DIR - the location of the trimmomatic jar
TRIMMOMATIC_JAR - the name of the jar file
TRIMMOMATIC_ADAPTERS_DIR - location of adapters

This is with planemo 0.22.2 and a fresh $HOME/.planemo.

Any ideas?

Peter



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/



--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size

[rbrown1422]

Good morning team,

I have an Rscript tool that is trying to read a file I uploaded into the 
history beforehand.  Galaxy is running with the same user and privileges as the 
dataset directory.

Rscript --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/Foo/Foo.R 
--args $inputFile1 . 

Why would this be?

Error in file(file, "rt") : cannot open the connectionCalls: 
performDataOrdering -> read.table -> fileIn addition: Warning message:In 
file(file, "rt") :  cannot open file 
'--file=/home/rbrown/hmgalaxy/database/files/000/dataset_162.dat': No such file 
or directoryExecution halted

When I try to run as R versus Rscript - I get a syntax error about unexpected 
'(' on function call that works fine in R window.

ThanksBob

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] dramm.py error

[Le-shin Wu]

Hi,

I was trying to setup a galaxy server and connect to our UGE cluster. If I
setup the default job runner as "local", our galaxy server works properly.
But if I change the default job runner as "drmaa", our galaxy server throws
out the following error message. It looks like drmaa.py has unicode
decoding issue. I wonder does someone have the same problem before and how
can I fix it. The python version we are using is 2.7.10.  Thank you.

galaxy.jobs.runners ERROR 2016-02-04 10:49:44,689 (3) Unhandled exception
calling queue_job
Traceback (most recent call last):
  File "/home/c226089/galaxy/lib/galaxy/jobs/runners/__init__.py", line
103, in run_next
method(arg)
  File "/home/c226089/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 135,
in queue_job
job_name = ''.join( map( lambda x: x if x in ( string.letters +
string.digits + '_' ) else '_', job_name ) )
  File "/home/c226089/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 135,
in 
job_name = ''.join( map( lambda x: x if x in ( string.letters +
string.digits + '_' ) else '_', job_name ) )
UnicodeDecodeError: 'ascii' codec can't decode byte 0xaa in position 52:
ordinal not in range(128)


Best

LW
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size

[John Chilton]

Forgot to cc the mailing list.

-John

On Thu, Feb 4, 2016 at 8:11 PM, John Chilton  wrote:
> Are you sure about the --file when calling Rscript?
>
> Here is the usage for my local version which does not expect an
> argument named --file:
>
> Usage: /path/to/Rscript [--options] [-e expr] file [args]
>
> --options accepted are
>   --help  Print usage and exit
>   --version   Print version and exit
>   --verbose   Print information on progress
>   --default-packages=list
>   Where 'list' is a comma-separated set
> of package names, or 'NULL'
> or options to R, in addition to --slave --no-restore, such as
>   --save  Do save workspace at the end of the session
>   --no-environDon't read the site and user environment files
>   --no-site-file  Don't read the site-wide Rprofile
>   --no-init-file  Don't read the user R profile
>   --restore   Do restore previously saved objects at startup
>   --vanilla   Combine --no-save, --no-restore, --no-site-file
> --no-init-file and --no-environ
>
> 'file' may contain spaces but not shell metacharacters
>
> Also, instead of using $GALAXY_ROOT - I would use $__tool_directory__
> if the tool XML file is located next to the RScript, like this:
>
> $__tool_directory__/Foo.R
>
> -John
>
>
> On Thu, Feb 4, 2016 at 7:05 PM,   wrote:
>> Good morning team,
>> I have an Rscript tool that is trying to read a file I uploaded into the
>> history beforehand.  Galaxy is running with the same user and privileges as
>> the dataset directory.
>> Rscript --slave --vanilla
>> --file=$GALAXY_ROOT_DIR/tools/Foo/Foo.R --args $inputFile1 . 
>> Why would this be?
>>
>> Error in file(file, "rt") : cannot open the connection
>> Calls: performDataOrdering -> read.table -> file
>> In addition: Warning message:
>> In file(file, "rt") :
>>   cannot open file
>> '--file=/home/rbrown/hmgalaxy/database/files/000/dataset_162.dat': No such
>> file or directory
>> Execution halted
>>
>> When I try to run as R versus Rscript - I get a syntax error about
>> unexpected '(' on function call that works fine in R window.
>>
>> Thanks
>> Bob
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size

[rbrown1422]

John,

Thanks for the great info.  I got the R to work not the Rscript.

However, my data files return RED even though there is data in them 

I am still getting R warning but no errors


During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_COLLATE failed, using "C" 
3: Setting LC_TIME failed, using "C" 
4: Setting LC_MESSAGES failed, using "C" 
5: Setting LC_MONETARY failed, using "C" 
6: Setting LC_PAPER failed, using "C" 
7: Setting LC_MEASUREMENT failed, using "C" 



Is there a flag I can set to igrore these warning and have Galaxy return GREEN?

thanks.
bob

- Original Message -From: John Chilton To: 
rbrown1...@comcast.net, galaxy-dev@lists.galaxyproject.orgSent: Thu, 04 Feb 
2016 20:11:53 - (UTC)Subject: Re: [galaxy-dev] Fwd: Rscript run under Tools 
Directory cannot see Datafile in History smaller email size

Forgot to cc the mailing list.

-John

On Thu, Feb 4, 2016 at 8:11 PM, John Chilton  wrote:> Are 
you sure about the --file when calling Rscript?>> Here is the usage for my 
local version which does not expect an> argument named --file:>> Usage: 
/path/to/Rscript [--options] [-e expr] file [args]>> --options accepted are> 
--help Print usage and exit> --version Print version and exit> --verbose Print 
information on progress> --default-packages=list> Where 'list' is a 
comma-separated set> of package names, or 'NULL'> or options to R, in addition 
to --slave --no-restore, such as> --save Do save workspace at the end of the 
session> --no-environ Don't read the site and user environment files> 
--no-site-file Don't read the site-wide Rprofile> --no-init-file Don't read the 
user R profile> --restore Do restore previously saved objects at startup> 
--vanilla Combine --no-save, --no-restore, --no-site-file> --no-init-file and 
--no-environ>> 'file' may contain spaces but not shell metacharacters>> Also, 
instead of using $GALAXY_ROOT - I would use $__tool_directory__> if the tool 
XML file is located next to the RScript, like this:>> 
$__tool_directory__/Foo.R>> -John>>> On Thu, Feb 4, 2016 at 7:05 PM, 
 wrote:>> Good morning team,>> I have an Rscript tool 
that is trying to read a file I uploaded into the>> history beforehand. Galaxy 
is running with the same user and privileges as>> the dataset directory.>> 
Rscript --slave --vanilla>> --file=$GALAXY_ROOT_DIR/tools/Foo/Foo.R 
--args $inputFile1 . >> Why would this be? Error in 
file(file, "rt") : cannot open the connection>> Calls: performDataOrdering -> 
read.table -> file>> In addition: Warning message:>> In file(file, "rt") :>> 
cannot open file>> 
'--file=/home/rbrown/hmgalaxy/database/files/000/dataset_162.dat': No such>> 
file or directory>> Execution halted When I try to run as R versus Rscript 
- I get a syntax error about>> unexpected '(' on function call that works fine 
in R window. Thanks>> Bob>> 
___>> Please keep all 
replies on the list by using "reply all">> in your mail client. To manage your 
subscriptions to this>> and other Galaxy lists, please use the interface at:>> 
https://lists.galaxyproject.org/ To search Galaxy mailing lists use the 
unified search at:>> http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/