Re: [galaxy-dev] "Edit attributes" for interval dataset not consistent with documentation

[nsora...@tiscali.it]

Dear Peter,this bug has been recently reported in 
https://github.com/galaxyproject/galaxy/issues/4966 and fixed in 
https://github.com/galaxyproject/galaxy/pull/5027 for the upcoming 18.01 Galaxy 
release.Not sure if this is worth a backport, but if you need it for 17.09 and 
want to try, it should be feasible.
Cheers,Nicola
-- Messaggio originale--Da: Peter BriggsData: gio 18 gen 2018 12:11A: 
galaxy-dev@lists.galaxyproject.org;CC: Oggetto:[galaxy-dev] "Edit attributes" 
for interval dataset not consistent with documentation
Dear Devs

One of my local users has noticed that the "edit attributes" function for 
"interval"-type datasets is not consistent with the documentation at:

https://galaxyproject.org/learn/datatypes/#interval

This states that only CHROM, START, and END are required, with the implication 
that other fields are optional.

However when editing the attributes for a dataset, if either of "Strand" or 
"Name" are not set to an explicit column number then "Save attributes" fails 
with the message: "Error occurred while saving. Please fill all the required 
fields and try again."

This is true on both our local Galaxy running release_17.09 and also on Galaxy 
main.

Is this a bug in the documentation, or the implementation?

Thanks,

Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Re: [galaxy-dev] Cluster Install Path Errors

[John Letaw]

Hi Nate,

Ah, I like this answer, let me see if I can make it work.  The way I currently 
have the instance set up is inside an Ubuntu 14.04 VM, that has been configured 
to accept lustre mounts.  The galaxy code is installed in a lustre directory, 
which I mainly did to avoid any issues with the cluster seeing important files. 
 I figure the installation may need to be moved to a local VM directory, with 
the Galaxy files visible in a lustre directory.  Anyways, the cluster itself is 
based on CentOS 7.  If you have any other suggestions for this type of setup, 
please let me know before I go too deep in the rabbit hole!

Cao – I can see hashlib in all of the correct places, but I will try to mess 
with the installation if the virtualenv method doesn’t help me.

Thanks so much!

From: Nate Coraor 
Date: Thursday, January 18, 2018 at 1:12 PM
To: Cao Tang 
Cc: John Letaw , galaxy-dev 
Subject: Re: [galaxy-dev] Cluster Install Path Errors

I think this error most commonly occurs when a virtualenv is used with a 
different python than the one it was created with. Is the cluster also running 
Ubuntu 14.04? If not, you can create a separate virtualenv for running tools 
using the instructions at:

https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#managing-dependencies-manually

Once created, your tools can use it by setting `/path/to/venv` on the destination in 
job_conf.xml

--nate

On Thu, Jan 18, 2018 at 1:50 PM, Cao Tang 
> wrote:
You can try to install:

https://pypi.python.org/pypi/hashlib

On Thu, Jan 18, 2018 at 1:22 PM, John Letaw 
> wrote:
Thanks for the response Peter.  I currently have this instance installed on a 
lustre fs, that is visible on an Ubuntu 14.04 vm.  So, there very well may be 
mismatches between directories on the VM, and those on the lustre cluster.  
This would mean the python installation on the VM needs to exactly match that 
which is on the cluster?  What else will need to match to ensure success?

Thanks,
John

On 1/18/18, 1:50 AM, "Peter Cock" 
> wrote:

I *think* this is a problem with your copy of Python 2.7 and a
standard library (hashlib) normally present. Do you know how this
Python was installed? If it was compiled from source, then it may have
been missing a few dependencies, and thus you have ended up with
missing a few normally present Python modules.

Peter

On Wed, Jan 17, 2018 at 11:15 PM, John Letaw 
> wrote:
> Hi all,
>
>
>
> I have been trying to finish up a production cluster Galaxy installation,
> and am having trouble with the below error.  In the past, when seeing
> something along these lines, I usually can adjust environmental variables
> either in startup scripts, or by including a script for Galaxy to source
> before it sends out a job.  I have tried all of these different methods, 
but
> I can’t seem to get rid of this error message in any tool invocation.  I
> currently have “embed_metadata_in_job” set to False in my job_conf.xml 
file.
> This removes a “No module named galaxy_ext.metadata.set_metadata” error, 
but
> this hashlib error remains.  If I could understand a little more about the
> steps that are taken when sending out a job, perhaps I could better 
diagnose
> this?
>
>
>
> “””
>
> Could not find platform dependent libraries
>
> Consider setting $PYTHONHOME to [:]
>
> Traceback (most recent call last):
>
>   File "~/galaxydev/galaxy/tools/data_source/upload.py", line 14, in
>
> import tempfile
>
>   File "/usr/lib64/python2.7/tempfile.py", line 35, in
>
> from random import Random as _Random
>
>  File "/usr/lib64/python2.7/random.py", line 49, in
>
> import hashlib as _hashlib
>
>   File "/usr/lib64/python2.7/hashlib.py", line 116, in
>
> import _hashlib
>
> ImportError: No module named _hashlib
>
> “””
>
>
>
> Thanks,
>
> John
>
>
> ___
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Re: [galaxy-dev] Cluster Install Path Errors

[Nate Coraor]

I think this error most commonly occurs when a virtualenv is used with a
different python than the one it was created with. Is the cluster also
running Ubuntu 14.04? If not, you can create a separate virtualenv for
running tools using the instructions at:

https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#managing-dependencies-manually

Once created, your tools can use it by setting `/path/to/venv` on the destination in
job_conf.xml

--nate

On Thu, Jan 18, 2018 at 1:50 PM, Cao Tang  wrote:

> You can try to install:
>
> https://pypi.python.org/pypi/hashlib
>
> On Thu, Jan 18, 2018 at 1:22 PM, John Letaw  wrote:
>
>> Thanks for the response Peter.  I currently have this instance installed
>> on a lustre fs, that is visible on an Ubuntu 14.04 vm.  So, there very well
>> may be mismatches between directories on the VM, and those on the lustre
>> cluster.  This would mean the python installation on the VM needs to
>> exactly match that which is on the cluster?  What else will need to match
>> to ensure success?
>>
>> Thanks,
>> John
>>
>> On 1/18/18, 1:50 AM, "Peter Cock"  wrote:
>>
>> I *think* this is a problem with your copy of Python 2.7 and a
>> standard library (hashlib) normally present. Do you know how this
>> Python was installed? If it was compiled from source, then it may have
>> been missing a few dependencies, and thus you have ended up with
>> missing a few normally present Python modules.
>>
>> Peter
>>
>> On Wed, Jan 17, 2018 at 11:15 PM, John Letaw  wrote:
>> > Hi all,
>> >
>> >
>> >
>> > I have been trying to finish up a production cluster Galaxy
>> installation,
>> > and am having trouble with the below error.  In the past, when
>> seeing
>> > something along these lines, I usually can adjust environmental
>> variables
>> > either in startup scripts, or by including a script for Galaxy to
>> source
>> > before it sends out a job.  I have tried all of these different
>> methods, but
>> > I can’t seem to get rid of this error message in any tool
>> invocation.  I
>> > currently have “embed_metadata_in_job” set to False in my
>> job_conf.xml file.
>> > This removes a “No module named galaxy_ext.metadata.set_metadata”
>> error, but
>> > this hashlib error remains.  If I could understand a little more
>> about the
>> > steps that are taken when sending out a job, perhaps I could better
>> diagnose
>> > this?
>> >
>> >
>> >
>> > “””
>> >
>> > Could not find platform dependent libraries
>> >
>> > Consider setting $PYTHONHOME to [:]
>> >
>> > Traceback (most recent call last):
>> >
>> >   File "~/galaxydev/galaxy/tools/data_source/upload.py", line 14,
>> in
>> >
>> > import tempfile
>> >
>> >   File "/usr/lib64/python2.7/tempfile.py", line 35, in
>> >
>> > from random import Random as _Random
>> >
>> >  File "/usr/lib64/python2.7/random.py", line 49, in
>> >
>> > import hashlib as _hashlib
>> >
>> >   File "/usr/lib64/python2.7/hashlib.py", line 116, in
>> >
>> > import _hashlib
>> >
>> > ImportError: No module named _hashlib
>> >
>> > “””
>> >
>> >
>> >
>> > Thanks,
>> >
>> > John
>> >
>> >
>> > ___
>> > 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/
>>
>>
>> ___
>> 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/
>
>
>
> ___
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>
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Re: [galaxy-dev] Cluster Install Path Errors

[Cao Tang]

You can try to install:

https://pypi.python.org/pypi/hashlib

On Thu, Jan 18, 2018 at 1:22 PM, John Letaw  wrote:

> Thanks for the response Peter.  I currently have this instance installed
> on a lustre fs, that is visible on an Ubuntu 14.04 vm.  So, there very well
> may be mismatches between directories on the VM, and those on the lustre
> cluster.  This would mean the python installation on the VM needs to
> exactly match that which is on the cluster?  What else will need to match
> to ensure success?
>
> Thanks,
> John
>
> On 1/18/18, 1:50 AM, "Peter Cock"  wrote:
>
> I *think* this is a problem with your copy of Python 2.7 and a
> standard library (hashlib) normally present. Do you know how this
> Python was installed? If it was compiled from source, then it may have
> been missing a few dependencies, and thus you have ended up with
> missing a few normally present Python modules.
>
> Peter
>
> On Wed, Jan 17, 2018 at 11:15 PM, John Letaw  wrote:
> > Hi all,
> >
> >
> >
> > I have been trying to finish up a production cluster Galaxy
> installation,
> > and am having trouble with the below error.  In the past, when seeing
> > something along these lines, I usually can adjust environmental
> variables
> > either in startup scripts, or by including a script for Galaxy to
> source
> > before it sends out a job.  I have tried all of these different
> methods, but
> > I can’t seem to get rid of this error message in any tool
> invocation.  I
> > currently have “embed_metadata_in_job” set to False in my
> job_conf.xml file.
> > This removes a “No module named galaxy_ext.metadata.set_metadata”
> error, but
> > this hashlib error remains.  If I could understand a little more
> about the
> > steps that are taken when sending out a job, perhaps I could better
> diagnose
> > this?
> >
> >
> >
> > “””
> >
> > Could not find platform dependent libraries
> >
> > Consider setting $PYTHONHOME to [:]
> >
> > Traceback (most recent call last):
> >
> >   File "~/galaxydev/galaxy/tools/data_source/upload.py", line 14, in
> >
> > import tempfile
> >
> >   File "/usr/lib64/python2.7/tempfile.py", line 35, in
> >
> > from random import Random as _Random
> >
> >  File "/usr/lib64/python2.7/random.py", line 49, in
> >
> > import hashlib as _hashlib
> >
> >   File "/usr/lib64/python2.7/hashlib.py", line 116, in
> >
> > import _hashlib
> >
> > ImportError: No module named _hashlib
> >
> > “””
> >
> >
> >
> > Thanks,
> >
> > John
> >
> >
> > ___
> > 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/
>
>
> ___
> 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:
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>
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Re: [galaxy-dev] Cluster Install Path Errors

[John Letaw]

Thanks for the response Peter.  I currently have this instance installed on a 
lustre fs, that is visible on an Ubuntu 14.04 vm.  So, there very well may be 
mismatches between directories on the VM, and those on the lustre cluster.  
This would mean the python installation on the VM needs to exactly match that 
which is on the cluster?  What else will need to match to ensure success?

Thanks,
John

On 1/18/18, 1:50 AM, "Peter Cock"  wrote:

I *think* this is a problem with your copy of Python 2.7 and a
standard library (hashlib) normally present. Do you know how this
Python was installed? If it was compiled from source, then it may have
been missing a few dependencies, and thus you have ended up with
missing a few normally present Python modules.

Peter

On Wed, Jan 17, 2018 at 11:15 PM, John Letaw  wrote:
> Hi all,
>
>
>
> I have been trying to finish up a production cluster Galaxy installation,
> and am having trouble with the below error.  In the past, when seeing
> something along these lines, I usually can adjust environmental variables
> either in startup scripts, or by including a script for Galaxy to source
> before it sends out a job.  I have tried all of these different methods, 
but
> I can’t seem to get rid of this error message in any tool invocation.  I
> currently have “embed_metadata_in_job” set to False in my job_conf.xml 
file.
> This removes a “No module named galaxy_ext.metadata.set_metadata” error, 
but
> this hashlib error remains.  If I could understand a little more about the
> steps that are taken when sending out a job, perhaps I could better 
diagnose
> this?
>
>
>
> “””
>
> Could not find platform dependent libraries
>
> Consider setting $PYTHONHOME to [:]
>
> Traceback (most recent call last):
>
>   File "~/galaxydev/galaxy/tools/data_source/upload.py", line 14, in
>
> import tempfile
>
>   File "/usr/lib64/python2.7/tempfile.py", line 35, in
>
> from random import Random as _Random
>
>  File "/usr/lib64/python2.7/random.py", line 49, in
>
> import hashlib as _hashlib
>
>   File "/usr/lib64/python2.7/hashlib.py", line 116, in
>
> import _hashlib
>
> ImportError: No module named _hashlib
>
> “””
>
>
>
> Thanks,
>
> John
>
>
> ___
> 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/


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Re: [galaxy-dev] No legal value defined in a planemo test for param type="select" and options="from_file"

[Olivier Inizan]

Thank you Peter !

If I have well understood the workaround implies having a local galaxy instance 
with the .loc file.
But for a planemo test with Travis CI I still will have the error.
Is it correct ?

Thanks again Peter.

Olivier



Olivier INIZAN
olivier.ini...@inra.fr
Unité Mathématiques & Informatique Appliquées du Génome à l'Environnement
Plateforme bioinformatique Migale
Bâtiment 233
Domaine de Vilvert
78352 Jouy-en-Josas

Le 17 janv. 2018 à 17:39, Peter Cock 
> a écrit :

It sounds like it could be this issue?:

https://github.com/galaxyproject/planemo/issues/530

If so, the good news is there is a workaround (see issue discussion).

Peter

On Wed, Jan 17, 2018 at 4:24 PM, Olivier Inizan  wrote:
Dear list,

I am trying to write a test with a param type "select" and options
"from_file".
I have the following param section in the wrapper:



   
   
   
   



And I  wrote the following test section:

   ...
   


The planemo test command failed with the following message:
RunToolException: Error creating a job for these tool inputs - Parameter
ref_file requires a value, but has no legal values defined.

Looking at the planemo documentation I saw the entry "test index (.loc)
data":
http://planemo.readthedocs.io/en/latest/writing_how_do_i.html#test-index-loc-data
but it seems to work with .

Have you any test example working with  ?

Thanks for your help.

Olivier


Olivier INIZAN
olivier.ini...@inra.fr
Unité Mathématiques & Informatique Appliquées du Génome à l'Environnement
Plateforme bioinformatique Migale
Bâtiment 233
Domaine de Vilvert
78352 Jouy-en-Josas


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Re: [galaxy-dev] upload from dropbox

[Matthias Bernt]

Hi Curtis,

thanks for your comments. In addition I found out that wget works 
irrespective of the suffix. So setting the user agent might also help. I 
opened an issue and wait for some comments:


https://github.com/galaxyproject/galaxy/issues/5330

Best,
Matthias


On 17.01.2018 20:38, Hendrickson, Curtis (Campus) wrote:

Matthias,

The default link generated by dropbox ends in http….?dl=0, which brings 
up a webpage with a download option.

To get a direct download, change the suffix to ?dl=1

Perhaps you could even hack galaxy’s upload script to recognize these 
URLs and patch them on the fly - that would be a public service to us all.


Example:

View in a web page (default link generated by system right-click or 
other dropbox bits):

_https://www.dropbox.com/s/lqsz785od3rxzhv/hello.txt?dl=0_
Download raw file:
https://www.dropbox.com/s/lqsz785od3rxzhv/hello.txt?dl= 
1


I pasted this URL into usegalaxy.org , set data 
type to tabular, and it worked fine: 
https://usegalaxy.org/u/curtish-uab/h/dropboxcom-test



Regards,
Curtis

On Jan 16, 2018, at 8:12 AM, Matthias Bernt > wrote:


Dear list and a happy new year,

does anyone has experience with upload from dropbox to galaxy (by 
pasting the shared link)? I always get an empty dataset with the 
additional info "The uploaded file contains inappropriate HTML content".


I guess the dropbox download link is not actually a real download link 
but a link to a website that contains some javascript button that 
starts the download...


Best,
Matthias


--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de , www.ufz.de 

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: 
MinDirig Wilfried Kraus

Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
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--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: 
MinDirig Wilfried Kraus

Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
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[galaxy-dev] "Edit attributes" for interval dataset not consistent with documentation

[Peter Briggs]

Dear Devs

One of my local users has noticed that the "edit attributes" function for 
"interval"-type datasets is not consistent with the documentation at:

https://galaxyproject.org/learn/datatypes/#interval

This states that only CHROM, START, and END are required, with the implication 
that other fields are optional.

However when editing the attributes for a dataset, if either of "Strand" or 
"Name" are not set to an explicit column number then "Save attributes" fails 
with the message: "Error occurred while saving. Please fill all the required 
fields and try again."

This is true on both our local Galaxy running release_17.09 and also on Galaxy 
main.

Is this a bug in the documentation, or the implementation?

Thanks,

Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Re: [galaxy-dev] No legal value defined in a planemo test for param type="select" and options="from_file"

[Peter Cock]

You can still use the workaround on TravisCI by creating a Galaxy
instance and telling planemo to use it (rather than the default of
letting planemo create the test Galaxy instance).

I do this here for example:

https://github.com/peterjc/pico_galaxy/blob/e2fa1c599b6670b418479447fe5a181a97a6c834/.travis.yml#L126

Peter

On Thu, Jan 18, 2018 at 11:21 AM, Olivier Inizan  wrote:
> Thank you Peter !
>
> If I have well understood the workaround implies having a local galaxy
> instance with the .loc file.
> But for a planemo test with Travis CI I still will have the error.
> Is it correct ?
>
> Thanks again Peter.
>
> Olivier
>
>
>
> Olivier INIZAN
> olivier.ini...@inra.fr
> Unité Mathématiques & Informatique Appliquées du Génome à l'Environnement
> Plateforme bioinformatique Migale
> Bâtiment 233
> Domaine de Vilvert
> 78352 Jouy-en-Josas
>
> Le 17 janv. 2018 à 17:39, Peter Cock  a écrit :
>
> It sounds like it could be this issue?:
>
> https://github.com/galaxyproject/planemo/issues/530
>
> If so, the good news is there is a workaround (see issue discussion).
>
> Peter
>
> On Wed, Jan 17, 2018 at 4:24 PM, Olivier Inizan 
> wrote:
>
> Dear list,
>
> I am trying to write a test with a param type "select" and options
> "from_file".
> I have the following param section in the wrapper:
>
> 
>  help="Select reference from the list">
>
>
>
>
> 
>
>
> And I  wrote the following test section:
> 
>...
>
> 
>
> The planemo test command failed with the following message:
> RunToolException: Error creating a job for these tool inputs - Parameter
> ref_file requires a value, but has no legal values defined.
>
> Looking at the planemo documentation I saw the entry "test index (.loc)
> data":
> http://planemo.readthedocs.io/en/latest/writing_how_do_i.html#test-index-loc-data
> but it seems to work with .
>
> Have you any test example working with  ?
>
> Thanks for your help.
>
> Olivier
>
>
> Olivier INIZAN
> olivier.ini...@inra.fr
> Unité Mathématiques & Informatique Appliquées du Génome à l'Environnement
> Plateforme bioinformatique Migale
> Bâtiment 233
> Domaine de Vilvert
> 78352 Jouy-en-Josas
>
>
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Re: [galaxy-dev] Cluster Install Path Errors

[Peter Cock]

I *think* this is a problem with your copy of Python 2.7 and a
standard library (hashlib) normally present. Do you know how this
Python was installed? If it was compiled from source, then it may have
been missing a few dependencies, and thus you have ended up with
missing a few normally present Python modules.

Peter

On Wed, Jan 17, 2018 at 11:15 PM, John Letaw  wrote:
> Hi all,
>
>
>
> I have been trying to finish up a production cluster Galaxy installation,
> and am having trouble with the below error.  In the past, when seeing
> something along these lines, I usually can adjust environmental variables
> either in startup scripts, or by including a script for Galaxy to source
> before it sends out a job.  I have tried all of these different methods, but
> I can’t seem to get rid of this error message in any tool invocation.  I
> currently have “embed_metadata_in_job” set to False in my job_conf.xml file.
> This removes a “No module named galaxy_ext.metadata.set_metadata” error, but
> this hashlib error remains.  If I could understand a little more about the
> steps that are taken when sending out a job, perhaps I could better diagnose
> this?
>
>
>
> “””
>
> Could not find platform dependent libraries
>
> Consider setting $PYTHONHOME to [:]
>
> Traceback (most recent call last):
>
>   File "~/galaxydev/galaxy/tools/data_source/upload.py", line 14, in
>
> import tempfile
>
>   File "/usr/lib64/python2.7/tempfile.py", line 35, in
>
> from random import Random as _Random
>
>  File "/usr/lib64/python2.7/random.py", line 49, in
>
> import hashlib as _hashlib
>
>   File "/usr/lib64/python2.7/hashlib.py", line 116, in
>
> import _hashlib
>
> ImportError: No module named _hashlib
>
> “””
>
>
>
> Thanks,
>
> John
>
>
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