Re: [galaxy-dev] automatic adding of a tab in a fastq header

[Martin Čech]

Thank you for all the help Peter!

Also this is already backported and fixed in 16.01

Sorry for causing this bug in the first place.
M.

On Tue, Mar 22, 2016, 18:29 Peter Cock  wrote:

> Well done for solving this Fabien, with only a small hint from me.
> I'm glad to see your suggested fix has already been applied to
> the Galaxy repository so should be in the next stable release.
>
> Thank you!
>
> Peter
>
> (Also thank you Martin, Nicola, Dan, etc)
>
>
> On Tue, Mar 22, 2016 at 8:43 PM, Martin Čech  wrote:
> > Thank you very much for solving this Fabien, The PR with your fix has
> been
> > created here: https://github.com/galaxyproject/galaxy/pull/1985
> >
> > Martin
> >
> >
> > On Mon, Mar 21, 2016 at 5:43 PM fmareuil  wrote:
> >>
> >> Hi Peter,
> >>
> >> I worked on it today and I found  the reason of this bug. In the
> upload.py
> >> tool, the existence of dataset.space_to_tab is tested. In the old
> version of
> >> the data library, when the option was unchecked, the value space_to_tab
> was
> >> None and the test worked. But in the new version the value of
> space_to_tab
> >> is "False", it's a string and the test "if dataset.space_to_tab" returns
> >> True.
> >> It is possible to fix it with a little correction of the
> >> "/lib/galaxy/webapps/galaxy/api/lda_datasets.py".
> >> I join a patch with this email.
> >> I can propose a pull request if you want.
> >>
> >> Best,
> >>
> >> Fabien
> >>
>
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Re: [galaxy-dev] automatic adding of a tab in a fastq header

[Peter Cock]

Well done for solving this Fabien, with only a small hint from me.
I'm glad to see your suggested fix has already been applied to
the Galaxy repository so should be in the next stable release.

Thank you!

Peter

(Also thank you Martin, Nicola, Dan, etc)


On Tue, Mar 22, 2016 at 8:43 PM, Martin Čech  wrote:
> Thank you very much for solving this Fabien, The PR with your fix has been
> created here: https://github.com/galaxyproject/galaxy/pull/1985
>
> Martin
>
>
> On Mon, Mar 21, 2016 at 5:43 PM fmareuil  wrote:
>>
>> Hi Peter,
>>
>> I worked on it today and I found  the reason of this bug. In the upload.py
>> tool, the existence of dataset.space_to_tab is tested. In the old version of
>> the data library, when the option was unchecked, the value space_to_tab was
>> None and the test worked. But in the new version the value of space_to_tab
>> is "False", it's a string and the test "if dataset.space_to_tab" returns
>> True.
>> It is possible to fix it with a little correction of the
>> "/lib/galaxy/webapps/galaxy/api/lda_datasets.py".
>> I join a patch with this email.
>> I can propose a pull request if you want.
>>
>> Best,
>>
>> Fabien
>>
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Re: [galaxy-dev] automatic adding of a tab in a fastq header

[Martin Čech]

Thank you very much for solving this Fabien, The PR with your fix has been
created here: https://github.com/galaxyproject/galaxy/pull/1985

Martin

On Mon, Mar 21, 2016 at 5:43 PM fmareuil  wrote:

> Hi Peter,
>
> I worked on it today and I found  the reason of this bug. In the upload.py
> tool, the existence of dataset.space_to_tab is tested. In the old version
> of the data library, when the option was unchecked, the value space_to_tab
> was None and the test worked. But in the new version the value of
> space_to_tab is "False", it's a string and the test "if
> dataset.space_to_tab" returns True.
> It is possible to fix it with a little correction of the
> "/lib/galaxy/webapps/galaxy/api/lda_datasets.py".
> I join a patch with this email.
> I can propose a pull request if you want.
>
> Best,
>
> Fabien
>
>
> --
> Fabien Mareuil | Centre d'Informatique pour la Biologie
> fabien.mare...@pasteur.fr | Institut Pasteur
> 25,28 rue du Docteur Roux 75015 Paris, France
>
>
> On 21/03/2016 09:45, fmareuil wrote:
>
> Hi Peter,
>
> I tested it on the last version of the dev and master branches.
>
> step-by-step :
> I click on the "shared data/Data Libraries", I select my library and I
> click on the button to upload a file and I select the option "from User
> Directory". I select my fastqsanger file (sequences headers are like this :
> @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC
> with a space between @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 and
> 1:N:0:ATGAGC and I import it (with or without the auto-detect option).
> When I look the file in a history, the space between
> @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 and 1:N:0:ATGAGC has been
> replaced by a tab.
>
> I didn't have this problem with "shared data/ Data Libraries deprecated".
>
> Thank a lot for your help,
> Best,
>
> Fabien
>
> On 18/03/2016 18:59, Peter Cock wrote:
>
> Can you provide more details - in particular the version of Galaxy you
> are running? A step-by-step description of how you did the data import
> might be useful too for the Galaxy team to try to reproduce this.
>
> Peter
>
> On Fri, Mar 18, 2016 at 5:34 PM, Fabien Mareuil 
>  wrote:
>
> Hi Peter,
>
> Thank a lot for this information, I didn't found this option for the new
> version of the Data Libraries.
> This could explain why there is this conversion.
> I tested it with an automatic format detection and when I set explicitly
> the
> format but in the two cases a tab was added.
>
> Fabien
>
>
> Le 18/03/2016 17:04, Peter Cock a écrit :
>
> Hi Fabien,
>
> There is a Galaxy upload option to turn spaces into tabs, useful for
> tables of data. Is that being ticked by mistake? That would explain
> this problem.
>
> Also I would check if the FASTQ file format is being detected
> automatically, or set explicitly (e.g. fastqsanger)? Doing that ought
> to prevent any changes.
>
> Peter
>
> On Fri, Mar 18, 2016 at 3:26 PM, Fabien Mareuil 
> 
> wrote:
>
> Hi,
>
> We got a problem with the new version of Data libraries. When we upload a
> fastq file from a User Directory, a tabulation character is added in the
> header in replacement of a space character.
>
> from @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC to
> @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965  1:N:0:ATGAGC
>
>
> This behavior causes an error with cutadapt 1.6 (maybe with other tools)
> because it doesn't work with tab character. With the direct upload tool
> or
> the deprecated version of Data Libraries no tab character is added. Do
> you
> have some idea to correct this problem? Thanks a lot Best regards --
> Fabien Mareuil | Centre d'Informatique pour la Biologie
> fabien.mare...@pasteur.fr | Institut Pasteur 25,28 rue du Docteur Roux
> 75015
> Paris, France
>
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[galaxy-dev] Troubleshooting BAM file upload issues

[Amelia Ireland]

I'm setting up a Galaxy instance on a new server and am having some issues
with BAM file uploads. I'm using the BAM files supplied with JBrowse for
testing purposes. I have Galaxy installed on my laptop and file uploads are
working fine, so it's evidently an issue with the server and/or OS
configuration.

Attempting to upload a BAM file returns the message

"The uploaded binary file contains inappropriate content"

and the upload is empty.

The server is running Scientific Linux and uses the Environment Modules
system for dependency management. I can successfully upload bed and bigwig
files, which suggests that samtools is being loaded and functioning
correctly.

If someone can suggest some troubleshooting steps, I would be most grateful.

Thanks!
Amelia

Integrated Microbial Genomics (IMG)
JGI / LBL
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[galaxy-dev] Numpy 1.9 installation errors

[Dewell, Scott]

Hi all - trying to install numpy 1.9 and getting the following error:

numpy 1.9 package Error Error installing tool dependency numpy version 1.9: 
'NoneType' object has no attribute 'prepare_step'


atlas 3.10.2 package Installed
numpy 1.9 package Error Error installing tool dependency numpy version 1.9: 
'NoneType' object has no attribute 'prepare_step'
python 2.7.10 package Installed

numpy 1.7 has installed successfully elsewhere. Thank you!
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Re: [galaxy-dev] "Edit settings" button in Trackster is no longer working (15.10)

[Hans-Rudolf Hotz]

Hi Carl

It works !
Thank you very much for providing  a fix so fast.


Regards, Hans-Rudolf

On 03/22/2016 02:26 PM, Carl Eberhard wrote:

https://github.com/galaxyproject/galaxy/pull/1972

Thanks for letting us know about this. Let me know if you spot any
problems with that fix.

On Tue, Mar 22, 2016 at 8:32 AM, Carl Eberhard > wrote:

Hey, Hans

Looks like a problem with the way we're loading the color-picker
library Farbtastic. I'll take a look, try to get a fix out, and
update here today.

Carl

On Mon, Mar 21, 2016 at 9:01 AM, Hans-Rudolf Hotz > wrote:

Hi all

Since we upgraded our Galaxy installation from 15.05 to 15.10
(plus the recent security fix, changeset: 17161:3f95c21b1a85),
the "Edit settings" button in Trackster is no longer working.
The window, which normally allows you to select the colors, etc.
doesn't show up anymore.

This happens with different browsers on mac and linux. On the
console I get: "TypeError: a.browser is undefined"

Has anyone else seen this problem? Or is there even already a
fix available?


Thank you very much for your help
Hans-Rudolf








--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] "Edit settings" button in Trackster is no longer working (15.10)

[Carl Eberhard]

https://github.com/galaxyproject/galaxy/pull/1972

Thanks for letting us know about this. Let me know if you spot any problems
with that fix.

On Tue, Mar 22, 2016 at 8:32 AM, Carl Eberhard 
wrote:

> Hey, Hans
>
> Looks like a problem with the way we're loading the color-picker library
> Farbtastic. I'll take a look, try to get a fix out, and update here today.
>
> Carl
>
> On Mon, Mar 21, 2016 at 9:01 AM, Hans-Rudolf Hotz  wrote:
>
>> Hi all
>>
>> Since we upgraded our Galaxy installation from 15.05 to 15.10 (plus the
>> recent security fix, changeset: 17161:3f95c21b1a85), the "Edit settings"
>> button in Trackster is no longer working. The window, which normally allows
>> you to select the colors, etc. doesn't show up anymore.
>>
>> This happens with different browsers on mac and linux. On the console I
>> get: "TypeError: a.browser is undefined"
>>
>> Has anyone else seen this problem? Or is there even already a fix
>> available?
>>
>>
>> Thank you very much for your help
>> Hans-Rudolf
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>>
>>
>>
>> Hans-Rudolf Hotz, PhD
>> Bioinformatics Support
>>
>> Friedrich Miescher Institute for Biomedical Research
>> Maulbeerstrasse 66
>> 4058 Basel/Switzerland
>> ___
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>
>
>
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Re: [galaxy-dev] shed_tool_conf.xml

[Hans-Rudolf Hotz]

On 03/22/2016 12:56 PM, Peter Cock wrote:

I would try validating the broken XML file (e.g. using an online tool,
or an XML aware editor). That might be enough to find the error and
fix it by hand.

I don't know if there is a clever way to regenerate the file instead...



probably a lot of 'manual' work including comparing with the admin page 
'Installed tool shed repositories'.


Also, look at the file "integrated_tool_panel.xml". all tools listed 
there which are not listed in "tool_conf.xml" need an entry in 
shed_tool_conf.xmlas far as I know.



Hans-Rudolf





Peter


On Tue, Mar 22, 2016 at 11:49 AM, Rathert, Philipp, Dr.
 wrote:

Dear all,


I think I made a really stupid mistake. I edited the shed_tool_con.xml file
to change the order and section of tools.


Doing this I might have introduced an error I cannot locate. However (now
comes the stupidity), I didn't save the old version of the
shed_tool_conf.xml file...


Is there a way to fix this or do I have to reinstall all tools again?


Thank you for your help.


cheers,


Philipp


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Re: [galaxy-dev] shed_tool_conf.xml

[Bjoern Gruening]

As Peter already mentioned a XML validator is a nice tool for this purpose.

For example this one:
http://www.xmlvalidation.com


A stupid way to do that is to remove the half bottom of your xml and 
open it using Firefox for example.

If OK

Add the half top of the half bottom -> firefox
If OK

…

If KO

Remove the half bottom of the remain -> firefox
..

It’s stupid but it’s often work :)


Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org 

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



Le 22 mars 2016 à 12:56, Peter Cock > a écrit :


I would try validating the broken XML file (e.g. using an online tool,
or an XML aware editor). That might be enough to find the error and
fix it by hand.

I don't know if there is a clever way to regenerate the file instead...

Peter


On Tue, Mar 22, 2016 at 11:49 AM, Rathert, Philipp, Dr.
> wrote:

Dear all,


I think I made a really stupid mistake. I edited the 
shed_tool_con.xml file

to change the order and section of tools.


Doing this I might have introduced an error I cannot locate. However 
(now

comes the stupidity), I didn't save the old version of the
shed_tool_conf.xml file...


Is there a way to fix this or do I have to reinstall all tools again?


Thank you for your help.


cheers,


Philipp


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Re: [galaxy-dev] shed_tool_conf.xml

[Rathert , Philipp , Dr .]

Hi Peter,



thx for the hint. Xcode was very helpful and I could localize the error.



However, this couldn't tell me why my label ids didn't work.

how do I implement those. Does this need a delimiter at the end like the 
sections?








Cheers,



Philipp

-Original message-
From: Peter Cock 
Sent: Tuesday 22nd March 2016 12:56
To: Rathert, Philipp, Dr. 
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] shed_tool_conf.xml


I would try validating the broken XML file (e.g. using an online tool,
or an XML aware editor). That might be enough to find the error and
fix it by hand.

I don't know if there is a clever way to regenerate the file instead...

Peter


On Tue, Mar 22, 2016 at 11:49 AM, Rathert, Philipp, Dr.
 wrote:
> Dear all,
>
>
> I think I made a really stupid mistake. I edited the shed_tool_con.xml file
> to change the order and section of tools.
>
>
> Doing this I might have introduced an error I cannot locate. However (now
> comes the stupidity), I didn't save the old version of the
> shed_tool_conf.xml file...
>
>
> Is there a way to fix this or do I have to reinstall all tools again?
>
>
> Thank you for your help.
>
>
> cheers,
>
>
> Philipp
>
>
> ___
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Re: [galaxy-dev] shed_tool_conf.xml

[Peter Cock]

I would try validating the broken XML file (e.g. using an online tool,
or an XML aware editor). That might be enough to find the error and
fix it by hand.

I don't know if there is a clever way to regenerate the file instead...

Peter


On Tue, Mar 22, 2016 at 11:49 AM, Rathert, Philipp, Dr.
 wrote:
> Dear all,
>
>
> I think I made a really stupid mistake. I edited the shed_tool_con.xml file
> to change the order and section of tools.
>
>
> Doing this I might have introduced an error I cannot locate. However (now
> comes the stupidity), I didn't save the old version of the
> shed_tool_conf.xml file...
>
>
> Is there a way to fix this or do I have to reinstall all tools again?
>
>
> Thank you for your help.
>
>
> cheers,
>
>
> Philipp
>
>
> ___
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[galaxy-dev] shed_tool_conf.xml

[Rathert , Philipp , Dr .]

Dear all,



I think I made a really stupid mistake. I edited the shed_tool_con.xml file to 
change the order and section of tools.



Doing this I might have introduced an error I cannot locate. However (now comes 
the stupidity), I didn't save the old version of the shed_tool_conf.xml file...



Is there a way to fix this or do I have to reinstall all tools again?



Thank you for your help.



cheers,



Philipp 

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Re: [galaxy-dev] mirDeep2 install error

[Jochen Bick]

Now it worked! I had to purge the old squid version 1.9g version because
it still recognised the old one to be not correctly installed...

Thanks Jochen

On 22.03.2016 11:26, Bjoern Gruening wrote:
> Can you remove and reinstall
> 
> package_randfold_2_0
> 
> Hopefully this solves your problem,
> Cheers,
> Bjoern
> 
> 
> On 22.03.2016 11:21, Jochen Bick wrote:
>> Hej Björn,
>>
>> so it did work in the development galaxy but not in our production
>> galaxy. Here I get the following error in package_randfold_2_0 after
>> successfully installing squid version 1.9g :
>>
>> randfold.c:24:18: error: squid.h: No such file or directory
>> randfold.c:26:23: error: sre_random.h: No such file or directory
>> randfold.c: In function 'main':
>> randfold.c:30: error: 'SQFILE' undeclared (first use in this function)
>> randfold.c:30: error: (Each undeclared identifier is reported only once
>> randfold.c:30: error: for each function it appears in.)
>> randfold.c:30: error: 'sqfp' undeclared (first use in this function)
>> randfold.c:38: error: 'SQINFO' undeclared (first use in this function)
>> randfold.c:38: error: expected ';' before 'sqinfo'
>> randfold.c:89: warning: incompatible implicit declaration of built-in
>> function 'strcpy'
>> randfold.c:96: error: 'SQFILE_FASTA' undeclared (first use in this
>> function)
>> randfold.c:100: error: 'sqinfo' undeclared (first use in this function)
>> randfold.c:103: warning: incompatible implicit declaration of built-in
>> function 'malloc'
>> randfold.c:103: warning: incompatible implicit declaration of built-in
>> function 'strlen'
>> randfold.c:136: warning: incompatible implicit declaration of built-in
>> function 'fabs'
>> randfold.c:158: warning: incompatible implicit declaration of built-in
>> function 'free'
>> make: *** [randfold] Error 1
>>
>> Cheer Jochen
>>
>>
>> ___
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Re: [galaxy-dev] mirDeep2 install error

[Jochen Bick]

Hej Björn,

so it did work in the development galaxy but not in our production
galaxy. Here I get the following error in package_randfold_2_0 after
successfully installing squid version 1.9g :

randfold.c:24:18: error: squid.h: No such file or directory
randfold.c:26:23: error: sre_random.h: No such file or directory
randfold.c: In function 'main':
randfold.c:30: error: 'SQFILE' undeclared (first use in this function)
randfold.c:30: error: (Each undeclared identifier is reported only once
randfold.c:30: error: for each function it appears in.)
randfold.c:30: error: 'sqfp' undeclared (first use in this function)
randfold.c:38: error: 'SQINFO' undeclared (first use in this function)
randfold.c:38: error: expected ';' before 'sqinfo'
randfold.c:89: warning: incompatible implicit declaration of built-in
function 'strcpy'
randfold.c:96: error: 'SQFILE_FASTA' undeclared (first use in this function)
randfold.c:100: error: 'sqinfo' undeclared (first use in this function)
randfold.c:103: warning: incompatible implicit declaration of built-in
function 'malloc'
randfold.c:103: warning: incompatible implicit declaration of built-in
function 'strlen'
randfold.c:136: warning: incompatible implicit declaration of built-in
function 'fabs'
randfold.c:158: warning: incompatible implicit declaration of built-in
function 'free'
make: *** [randfold] Error 1

Cheer Jochen


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Re: [galaxy-dev] mirDeep2 install error

[Jochen Bick]

Thanks Björn, looks good!

Cheers Jochen

On 22.03.2016 10:46, Bjoern Gruening wrote:
> Hi Jochen,
> 
> can you please try again I updated the recipes.
> 
> Sorry for the inconvenience,
> Bjoern
> 
> On 22.03.2016 10:24, Jochen Bick wrote:
>> Hi,
>>
>> I tried to install suite_mirdeep_2_0. There is an error in the
>> dependencies of package_squid_1_9g the download link has change to
>> http://eddylab.org/software/squid/squid.tar.gz
>>
>> Cheers Jochen
>>
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Re: [galaxy-dev] mirDeep2 install error

[Bjoern Gruening]

Hi Jochen,

can you please try again I updated the recipes.

Sorry for the inconvenience,
Bjoern

On 22.03.2016 10:24, Jochen Bick wrote:

Hi,

I tried to install suite_mirdeep_2_0. There is an error in the
dependencies of package_squid_1_9g the download link has change to
http://eddylab.org/software/squid/squid.tar.gz

Cheers Jochen

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Re: [galaxy-dev] Python 2.7 vs 2.6 for galaxy after 16.01

[Sebastian Schaaf]

Same here for v2.7.11 on SLES 11. If you want to integrate as many modules
as possible at compilation time (we had to skip four unimportant ones in
the end) it may be painful with an older OS, but I assume CentOS is a bit
less recalcitrant than SLES.
We installed everything in home scheme, which requires proper setup of
environment variables like $PATH, $LD_LIBRARY_PATH, $PYTHONPATH, etc...
For us the trigger for switching the Python version was an issue with an
outdated OpenSSL (just days before the Galaxy announcement regarding the
coming deprecation of 2.6), so we included the reworked/conmpiled OpenSSL
libraries first. I would recommend the same for you, if your OpenSSL
package is  We Iocally compile 2.7.8 and keep it in a distinct location that our paths
> references.
>
> This is very easy and has worked well for us.
>
> Please excuse any typos -- Sent from my iPhone
>
>> On Mar 21, 2016, at 5:32 PM, Peter Cock 
>> wrote:
>>
>> Hi D. K.,
>>
>> We're currently trying a locally compiled Python 2.7 (from source)
>> under the shared Galaxy mount for use with a CentOS 6 cluster
>> and Galaxy server.
>>
>> This seems to be working once we got the $PATH working for
>> cluster jobs (initially they would try to set the Galaxy metadata
>> using the system Python 2.6, which would fail).
>>
>> I don't know if this is any easier than using the CenOS Software
>> Collections as suggested by Nicola, especially when it comes to
>> updating the OS.
>>
>> Peter
>>
>>> On Mon, Mar 21, 2016 at 5:59 PM, Nicola Soranzo 
>>> wrote:
>>> Hi Daniel,
>>> I've been using python27 from CentOS Software Collections for quite
>>> some
>>> time. It's a bit annoying because you have to remember to load it, but
>>> it is
>>> surely doable.
>>>
>>> Cheers,
>>> Nicola
>>>
>>>
>>> On 21/03/16 17:46, D K wrote:
>>>
>>> Hi Galaxy Devs,
>>>
>>> This may be premature but I read that for Galaxy after 16.01 that the
>>> plan
>>> is for python 2.6 to no longer be supported. I'm currently running
>>> CentOS
>>> 6.6 which uses python 2.6. In order to be able to use newer versions of
>>> Galaxy is my only option to upgrade to a newer version of CentOS? Is it
>>> possible to use Conda, RedHat Software Collections or some other
>>> similar
>>> method instead of doing this upgrade?
>>>
>>> Thanks!
>>>
>>>
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>>>
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-- 
Sebastian Schaaf, M.Sc. Bioinformatics
Faculty Coordinator NGS Infrastructure
Chair of Biometry and Bioinformatics
Department of Medical Informatics,
 Biometry and Epidemiology (IBE)
University of Munich
DKTK Munich
Marchioninistr. 15, K U1 808
D-81377 Munich (Germany)
Tel: +49 89 4400 77499

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[galaxy-dev] mirDeep2 install error

[Jochen Bick]

Hi,

I tried to install suite_mirdeep_2_0. There is an error in the
dependencies of package_squid_1_9g the download link has change to
http://eddylab.org/software/squid/squid.tar.gz

Cheers Jochen

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