Re: [galaxy-dev] Cloudman & AWS IAM_PROFILE support?

[Enis Afgan]

Hi Chris,
Using non-default VPCs are difficult to get going at the moment but work is
underway that should make that easier for starters and we can then look at
other issues that may arise. Is a user-defined VPC your typically scenario?
I remember you mentioning something about a highly isolated VPC at some
point but we never got far on that discussion.

On Tue, Mar 15, 2016 at 10:46 PM, Chris Dagdigian  wrote:

>
> Hi Ryan,
>
> I've never been able to get cloudman to function within a private VPC so
> if this is your architecture as well and you manage to make progress I'd be
> interested in learning your methods. Thanks!
>
> Regards,
> Chris
>
>
> Enis Afgan wrote:
>
>> Hi Ryan,
>> I'm not sure I really understand your question but CloudMan can run under
>> an IAM account - it is just necessary to give the IAM user permissions to
>> create EC2 and S3 resources. Let us know if that's not what you had in mind
>> or if you have any more questions.
>>
>> Cheers,
>> Enis
>>
>
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Re: [galaxy-dev] Cloudman & AWS IAM_PROFILE support?

[Ryan G]

We actually have galaxy running within a VPC now. The problem we're running 
into is that when ec2 instances get created they don't have an I_am profile 
attached to them so they can't get access to S3 resources. This should just be 
a parameter past to AWS when the instances get created to attach the Iam 
profile. I just need to know where the code for creating ec2 instances is and I 
can test it out. 

Please excuse any typos -- Sent from my iPhone

> On Mar 15, 2016, at 10:46 PM, Chris Dagdigian  wrote:
> 
> 
> Hi Ryan,
> 
> I've never been able to get cloudman to function within a private VPC so if 
> this is your architecture as well and you manage to make progress I'd be 
> interested in learning your methods. Thanks!
> 
> Regards,
> Chris
> 
> 
> Enis Afgan wrote:
>> Hi Ryan,
>> I'm not sure I really understand your question but CloudMan can run under an 
>> IAM account - it is just necessary to give the IAM user permissions to 
>> create EC2 and S3 resources. Let us know if that's not what you had in mind 
>> or if you have any more questions.
>> 
>> Cheers,
>> Enis
> 
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Re: [galaxy-dev] Cloudman & AWS IAM_PROFILE support?

[Chris Dagdigian]

Hi Ryan,

I've never been able to get cloudman to function within a private VPC so 
if this is your architecture as well and you manage to make progress I'd 
be interested in learning your methods. Thanks!


Regards,
Chris


Enis Afgan wrote:

Hi Ryan,
I'm not sure I really understand your question but CloudMan can run 
under an IAM account - it is just necessary to give the IAM user 
permissions to create EC2 and S3 resources. Let us know if that's not 
what you had in mind or if you have any more questions.


Cheers,
Enis


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Re: [galaxy-dev] Cloudman & AWS IAM_PROFILE support?

[Enis Afgan]

Hi Ryan,
I'm not sure I really understand your question but CloudMan can run under
an IAM account - it is just necessary to give the IAM user permissions to
create EC2 and S3 resources. Let us know if that's not what you had in mind
or if you have any more questions.

Cheers,
Enis

On Mon, Mar 14, 2016 at 1:56 PM, Ryan G  wrote:

> Hi - Does Cloudman support IAM_PROFILES?   We run our instances within a
> VPC and assign an IAM_PROFILE to the ec2 instances so that they have access
> to resouces.   Does Cloudman have this support?
>
>
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Re: [galaxy-dev] Please help fix toolshed repository: trtr

[Martin Čech]

Hi Lance,

it seems the whole .git/ folder got accidentally uploaded there and it
causes trouble. I recommend using the direct mercurial access (
https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr), delete the folder,
commit the change and push it to the TS repository.

Please let me know how it goes.

Martin

On Tue, Mar 15, 2016 at 4:54 PM Lance Parsons 
wrote:

> I was helping someone with their toolshed repository and we ran into an
> issue, there is an old folder "myTools" in the repository that we cannot
> delete. It has a second copy of the tool (inadvertently). However, when we
> upload a new version with Planemo, the directory remains. Attempts to
> delete it via the toolshed web interface result in internal server
> errors. Can an admin take a look?
>
> https://toolshed.g2.bx.psu.edu/view/mrvollger/trtr/13cad5d36301
>
>
> --
> Lance Parsons - Scientific Programmer
> Carl C. Icahn Laboratory - Room 136
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
>
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[galaxy-dev] Help with dynamic job destination

[Lance Parsons]

I'm trying to setup a dynamic job destination for bowtie2 so that it 
submits to a different destination if the `-a` option is set or the `-k` 
option is set to a high value. I've got things working, but the function 
I've written seems rather complicated and ugly. I was wondering if 
anyone had any advice on a better way to query job parameters. See the 
function here:


https://gist.github.com/lparsons/a4724b51afd9027e3c0e

Thanks in advance for any suggestions or comments.

--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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[galaxy-dev] Please help fix toolshed repository: trtr

[Lance Parsons]

I was helping someone with their toolshed repository and we ran into an 
issue, there is an old folder "myTools" in the repository that we cannot 
delete. It has a second copy of the tool (inadvertently). However, when 
we upload a new version with Planemo, the directory remains. Attempts to 
delete it via the toolshed web interface result in internal server 
errors. Can an admin take a look?


https://toolshed.g2.bx.psu.edu/view/mrvollger/trtr/13cad5d36301


--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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Re: [galaxy-dev] Job stuck in running state.

[John Chilton]

What kind of database backend are you using (postgres, myql, or the
default sqlite)?

If you are running many jobs - I would definitely encourage using postgres.

-John

On Sun, Mar 13, 2016 at 2:48 PM, Zuzanna K. Filutowska
 wrote:
> Dear All,
>
> I am running newest version of Galaxy with PBS and I am observing
> strange behaviour: some jobs that were finished on the queue system are
> still shown as running on Galaxy Web interface. Communication with PBS
> server seems to work fine all the time. Nothing interesting seems to be
> in logs despite debug being on:
> sqlalchemy.pool.QueuePool ERROR 2016-03-13 11:36:02,544 Error closing
> cursor
> Any ideas, what can be a problem?
>
> --
>
> Pozdrawiam,
>
> --
> Zuzanna K. Filutowska, HPC Systems Administrator
> Poznan Supercomputing and Networking Center
> Institute of Bioorganic Chemistry Polish Academy of Sciences
> Seize the day boys! Make your lifes extraordinary! --John Keating
>
>
> ___
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Re: [galaxy-dev] Trackster in 16.01 broken

[Lubos Klucar]

Great, thanks, all is working now!

all the best

Lubos

On 15. 3. 2016 19:48, Marius van den Beek wrote:

Hi Lubos,

I opened a Pull Request on
https://github.com/galaxyproject/galaxy/pull/1930, which should
hopefully fix the problem.
If you want to give it a try, you can do
`git fetch origin pull/1930/head:more_bytestring_for_pysam`
and
`git checkout more_bytestring_for_pysam`.
When the problem has been solved, you can switch back to release_16.01
by doing `git checkout release_16.01`.

Thanks for reporting the error,
Marius


On 15 March 2016 at 19:25, Marius van den Beek mailto:m.vandenb...@gmail.com>> wrote:

Yes, `git checkout release_16.01` should do it, but wait a second,
there might actually be a problem,
since ` File
"/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
line 892, in get_iterator`,
while the PR addresses 354-356!


On 15 March 2016 at 19:23, Lubos Klucar mailto:klu...@embnet.sk>> wrote:



On 15. 3. 2016 19:15, Marius van den Beek wrote:

Hi Lubos,

hmm, I'm surprised about this.
Just to make sure, you are on the release_16.01 branch?
(`git branch` should highlight release_16.01)
This PR hasn't been merged into dev yet.


Hi Marius,

it seems I need more help with git, not the Galaxy!. ;-) My git
branch gives me:

   dev
* master

How should I 'switch' to 16.01??..

regards

Lubos

Cheers,
Marius

On 15 March 2016 at 19:08, Lubos Klucar mailto:klu...@embnet.sk>
>> wrote:

 Dear Marius,

 thanks for help, but it looks our galaxy is up to date:

 remote: Counting objects: 111, done.
 remote: Compressing objects: 100% (23/23), done.
 remote: Total 111 (delta 82), reused 75 (delta 75),
pack-reused 13
 Receiving objects: 100% (111/111), 39.85 KiB, done.
 Resolving deltas: 100% (82/82), completed with 29 local
objects.
  >From https://github.com/galaxyproject/galaxy
 8423fe7..23c3300  dev-> origin/dev
 5a50a46..65a5b08  release_16.01 -> origin/release_16.01
 Already up-to-date.

 After Galaxy restart the problem still persist...

 all the best

 Lubos

 On 15. 3. 2016 18:59, Marius van den Beek wrote:

 Hello Lubos,

 this should be fixed with
https://github.com/galaxyproject/galaxy/pull/1897.
 If you pull in the latest changes (git pull) on the
 release_16.01 branch
 things should work again.

 Cheers,
 Marius

 On 15 March 2016 at 18:54, Lubos Klucar
mailto:klu...@embnet.sk>
 >
 

Re: [galaxy-dev] Trackster in 16.01 broken

[Marius van den Beek]

Hi Lubos,

I opened a Pull Request on https://github.com/galaxyproject/galaxy/pull/1930,
which should hopefully fix the problem.
If you want to give it a try, you can do
`git fetch origin pull/1930/head:more_bytestring_for_pysam`
and
`git checkout more_bytestring_for_pysam`.
When the problem has been solved, you can switch back to release_16.01 by
doing `git checkout release_16.01`.

Thanks for reporting the error,
Marius


On 15 March 2016 at 19:25, Marius van den Beek 
wrote:

> Yes, `git checkout release_16.01` should do it, but wait a second, there
> might actually be a problem,
> since ` File 
> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
> line 892, in get_iterator`,
> while the PR addresses 354-356!
>
>
> On 15 March 2016 at 19:23, Lubos Klucar  wrote:
>
>>
>>
>> On 15. 3. 2016 19:15, Marius van den Beek wrote:
>>
>>> Hi Lubos,
>>>
>>> hmm, I'm surprised about this.
>>> Just to make sure, you are on the release_16.01 branch?
>>> (`git branch` should highlight release_16.01)
>>> This PR hasn't been merged into dev yet.
>>>
>>>
>> Hi Marius,
>>
>> it seems I need more help with git, not the Galaxy!. ;-) My git branch
>> gives me:
>>
>>   dev
>> * master
>>
>> How should I 'switch' to 16.01??..
>>
>> regards
>>
>> Lubos
>>
>> Cheers,
>>> Marius
>>>
>>> On 15 March 2016 at 19:08, Lubos Klucar >> > wrote:
>>>
>>> Dear Marius,
>>>
>>> thanks for help, but it looks our galaxy is up to date:
>>>
>>> remote: Counting objects: 111, done.
>>> remote: Compressing objects: 100% (23/23), done.
>>> remote: Total 111 (delta 82), reused 75 (delta 75), pack-reused 13
>>> Receiving objects: 100% (111/111), 39.85 KiB, done.
>>> Resolving deltas: 100% (82/82), completed with 29 local objects.
>>>  >From https://github.com/galaxyproject/galaxy
>>> 8423fe7..23c3300  dev-> origin/dev
>>> 5a50a46..65a5b08  release_16.01 -> origin/release_16.01
>>> Already up-to-date.
>>>
>>> After Galaxy restart the problem still persist...
>>>
>>> all the best
>>>
>>> Lubos
>>>
>>> On 15. 3. 2016 18:59, Marius van den Beek wrote:
>>>
>>> Hello Lubos,
>>>
>>> this should be fixed with
>>> https://github.com/galaxyproject/galaxy/pull/1897.
>>> If you pull in the latest changes (git pull) on the
>>> release_16.01 branch
>>> things should work again.
>>>
>>> Cheers,
>>> Marius
>>>
>>> On 15 March 2016 at 18:54, Lubos Klucar >> 
>>> >> wrote:
>>>
>>>  Hi,
>>>
>>>  after upgrading from 15.10 to 16.01, the trackster
>>> visualisation
>>>  tool is partly defective. It can successfully show e.g. GFF
>>> tracks,
>>>  but after adding e.g. BAM track nothing is shown. The only
>>>  suspicious debug output I could get when loading
>>> non-working-track is:
>>>
>>>  galaxy.webapps.galaxy.api.datasets ERROR 2016-03-15
>>> 11:44:38,853
>>>  Error in dataset API at listing contents: Expected bytes,
>>> got
>>>  unicode: Expected bytes, got unicode
>>>  Traceback (most recent call last):
>>> File
>>>
>>>
>>> "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py",
>>>  line 66, in show
>>>   rval = self._data( trans, dataset, **kwd )
>>> File
>>>
>>>
>>> "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py",
>>>  line 235, in _data
>>>   ref_seq=region, mean_depth=mean_depth, **kwargs )
>>> File
>>>
>>>
>>> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
>>>  line 192, in get_data
>>>   iterator = self.get_iterator( data_file, chrom, start,
>>> end,
>>>  **kwargs )
>>> File
>>>
>>>
>>> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
>>>  line 892, in get_iterator
>>>   data = data_file.fetch( start=start, end=end,
>>> reference=chrom )
>>> File "pysam/calignmentfile.pyx", line 868, in
>>>  pysam.calignmentfile.AlignmentFile.fetch
>>> (pysam/calignmentfile.c:10170)
>>> File "pysam/calignmentfile.pyx", line 787, in
>>>  pysam.calignmentfile.AlignmentFile.parse_region
>>>  (pysam/calignmentfile.c:9605)
>>> File "pysam/calignmentfile.pyx", line 1576, in
>>>  pysam.calignmentfile.AlignmentFile.gettid
>>> (pysam/calignmentfile.c:16665)
>>> File "pysam/calignmentfile.pyx", line 640, in
>>>  pysam.calignmentfile.AlignmentFile.get_tid
>>> (pysam/calignmentfile.c:8208)
>>> File "pysam/cutils.pyx", li

Re: [galaxy-dev] Trackster in 16.01 broken

[Lubos Klucar]

Dear Marius,

thanks for help, but it looks our galaxy is up to date:

remote: Counting objects: 111, done.
remote: Compressing objects: 100% (23/23), done.
remote: Total 111 (delta 82), reused 75 (delta 75), pack-reused 13
Receiving objects: 100% (111/111), 39.85 KiB, done.
Resolving deltas: 100% (82/82), completed with 29 local objects.
From https://github.com/galaxyproject/galaxy
   8423fe7..23c3300  dev-> origin/dev
   5a50a46..65a5b08  release_16.01 -> origin/release_16.01
Already up-to-date.

After Galaxy restart the problem still persist...

all the best

Lubos

On 15. 3. 2016 18:59, Marius van den Beek wrote:

Hello Lubos,

this should be fixed with https://github.com/galaxyproject/galaxy/pull/1897.
If you pull in the latest changes (git pull) on the release_16.01 branch
things should work again.

Cheers,
Marius

On 15 March 2016 at 18:54, Lubos Klucar mailto:klu...@embnet.sk>> wrote:

Hi,

after upgrading from 15.10 to 16.01, the trackster visualisation
tool is partly defective. It can successfully show e.g. GFF tracks,
but after adding e.g. BAM track nothing is shown. The only
suspicious debug output I could get when loading non-working-track is:

galaxy.webapps.galaxy.api.datasets ERROR 2016-03-15 11:44:38,853
Error in dataset API at listing contents: Expected bytes, got
unicode: Expected bytes, got unicode
Traceback (most recent call last):
   File
"/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py",
line 66, in show
 rval = self._data( trans, dataset, **kwd )
   File
"/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py",
line 235, in _data
 ref_seq=region, mean_depth=mean_depth, **kwargs )
   File
"/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
line 192, in get_data
 iterator = self.get_iterator( data_file, chrom, start, end,
**kwargs )
   File
"/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
line 892, in get_iterator
 data = data_file.fetch( start=start, end=end, reference=chrom )
   File "pysam/calignmentfile.pyx", line 868, in
pysam.calignmentfile.AlignmentFile.fetch (pysam/calignmentfile.c:10170)
   File "pysam/calignmentfile.pyx", line 787, in
pysam.calignmentfile.AlignmentFile.parse_region
(pysam/calignmentfile.c:9605)
   File "pysam/calignmentfile.pyx", line 1576, in
pysam.calignmentfile.AlignmentFile.gettid (pysam/calignmentfile.c:16665)
   File "pysam/calignmentfile.pyx", line 640, in
pysam.calignmentfile.AlignmentFile.get_tid (pysam/calignmentfile.c:8208)
   File "pysam/cutils.pyx", line 106, in pysam.cutils.force_bytes
(pysam/cutils.c:2170)
TypeError: Expected bytes, got unicode

Any help to solve this problem would be highly appreciated!

many thanks
--

 Lubos Klucar
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--

Lubos Klucar

Institute of Molecular Biology
Slovak Academy of Science
Dubravska cesta 21
845 51  Bratislava 45
Slovakia

Tel.: +421 2 5930 7413
Fax.: +421 2 5930 7416
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Re: [galaxy-dev] Trackster in 16.01 broken

[Marius van den Beek]

Hello Lubos,

this should be fixed with https://github.com/galaxyproject/galaxy/pull/1897.
If you pull in the latest changes (`git pull`) on the release_16.01 branch
things should work again.

Cheers,
Marius

On 15 March 2016 at 18:59, Marius van den Beek 
wrote:

> Hello Lubos,
>
> this should be fixed with
> https://github.com/galaxyproject/galaxy/pull/1897.
> If you pull in the latest changes (git pull) on the release_16.01 branch
> things should work again.
>
> Cheers,
> Marius
>
> On 15 March 2016 at 18:54, Lubos Klucar  wrote:
>
>> Hi,
>>
>> after upgrading from 15.10 to 16.01, the trackster visualisation tool is
>> partly defective. It can successfully show e.g. GFF tracks, but after
>> adding e.g. BAM track nothing is shown. The only suspicious debug output I
>> could get when loading non-working-track is:
>>
>> galaxy.webapps.galaxy.api.datasets ERROR 2016-03-15 11:44:38,853 Error in
>> dataset API at listing contents: Expected bytes, got unicode: Expected
>> bytes, got unicode
>> Traceback (most recent call last):
>>   File
>> "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py", line
>> 66, in show
>> rval = self._data( trans, dataset, **kwd )
>>   File
>> "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py", line
>> 235, in _data
>> ref_seq=region, mean_depth=mean_depth, **kwargs )
>>   File
>> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
>> line 192, in get_data
>> iterator = self.get_iterator( data_file, chrom, start, end, **kwargs )
>>   File
>> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
>> line 892, in get_iterator
>> data = data_file.fetch( start=start, end=end, reference=chrom )
>>   File "pysam/calignmentfile.pyx", line 868, in
>> pysam.calignmentfile.AlignmentFile.fetch (pysam/calignmentfile.c:10170)
>>   File "pysam/calignmentfile.pyx", line 787, in
>> pysam.calignmentfile.AlignmentFile.parse_region
>> (pysam/calignmentfile.c:9605)
>>   File "pysam/calignmentfile.pyx", line 1576, in
>> pysam.calignmentfile.AlignmentFile.gettid (pysam/calignmentfile.c:16665)
>>   File "pysam/calignmentfile.pyx", line 640, in
>> pysam.calignmentfile.AlignmentFile.get_tid (pysam/calignmentfile.c:8208)
>>   File "pysam/cutils.pyx", line 106, in pysam.cutils.force_bytes
>> (pysam/cutils.c:2170)
>> TypeError: Expected bytes, got unicode
>>
>> Any help to solve this problem would be highly appreciated!
>>
>> many thanks
>> --
>>
>> Lubos Klucar
>> ___
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>>
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>>  http://galaxyproject.org/search/mailinglists/
>
>
>
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Re: [galaxy-dev] Trackster in 16.01 broken

[Marius van den Beek]

Hello Lubos,

this should be fixed with https://github.com/galaxyproject/galaxy/pull/1897.
If you pull in the latest changes (git pull) on the release_16.01 branch
things should work again.

Cheers,
Marius

On 15 March 2016 at 18:54, Lubos Klucar  wrote:

> Hi,
>
> after upgrading from 15.10 to 16.01, the trackster visualisation tool is
> partly defective. It can successfully show e.g. GFF tracks, but after
> adding e.g. BAM track nothing is shown. The only suspicious debug output I
> could get when loading non-working-track is:
>
> galaxy.webapps.galaxy.api.datasets ERROR 2016-03-15 11:44:38,853 Error in
> dataset API at listing contents: Expected bytes, got unicode: Expected
> bytes, got unicode
> Traceback (most recent call last):
>   File "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py",
> line 66, in show
> rval = self._data( trans, dataset, **kwd )
>   File "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py",
> line 235, in _data
> ref_seq=region, mean_depth=mean_depth, **kwargs )
>   File
> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
> line 192, in get_data
> iterator = self.get_iterator( data_file, chrom, start, end, **kwargs )
>   File
> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
> line 892, in get_iterator
> data = data_file.fetch( start=start, end=end, reference=chrom )
>   File "pysam/calignmentfile.pyx", line 868, in
> pysam.calignmentfile.AlignmentFile.fetch (pysam/calignmentfile.c:10170)
>   File "pysam/calignmentfile.pyx", line 787, in
> pysam.calignmentfile.AlignmentFile.parse_region
> (pysam/calignmentfile.c:9605)
>   File "pysam/calignmentfile.pyx", line 1576, in
> pysam.calignmentfile.AlignmentFile.gettid (pysam/calignmentfile.c:16665)
>   File "pysam/calignmentfile.pyx", line 640, in
> pysam.calignmentfile.AlignmentFile.get_tid (pysam/calignmentfile.c:8208)
>   File "pysam/cutils.pyx", line 106, in pysam.cutils.force_bytes
> (pysam/cutils.c:2170)
> TypeError: Expected bytes, got unicode
>
> Any help to solve this problem would be highly appreciated!
>
> many thanks
> --
>
> Lubos Klucar
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[galaxy-dev] Trackster in 16.01 broken

[Lubos Klucar]

Hi,

after upgrading from 15.10 to 16.01, the trackster visualisation tool is 
partly defective. It can successfully show e.g. GFF tracks, but after 
adding e.g. BAM track nothing is shown. The only suspicious debug output 
I could get when loading non-working-track is:


galaxy.webapps.galaxy.api.datasets ERROR 2016-03-15 11:44:38,853 Error 
in dataset API at listing contents: Expected bytes, got unicode: 
Expected bytes, got unicode

Traceback (most recent call last):
  File 
"/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py", line 
66, in show

rval = self._data( trans, dataset, **kwd )
  File 
"/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py", line 
235, in _data

ref_seq=region, mean_depth=mean_depth, **kwargs )
  File 
"/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py", 
line 192, in get_data

iterator = self.get_iterator( data_file, chrom, start, end, **kwargs )
  File 
"/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py", 
line 892, in get_iterator

data = data_file.fetch( start=start, end=end, reference=chrom )
  File "pysam/calignmentfile.pyx", line 868, in 
pysam.calignmentfile.AlignmentFile.fetch (pysam/calignmentfile.c:10170)
  File "pysam/calignmentfile.pyx", line 787, in 
pysam.calignmentfile.AlignmentFile.parse_region 
(pysam/calignmentfile.c:9605)
  File "pysam/calignmentfile.pyx", line 1576, in 
pysam.calignmentfile.AlignmentFile.gettid (pysam/calignmentfile.c:16665)
  File "pysam/calignmentfile.pyx", line 640, in 
pysam.calignmentfile.AlignmentFile.get_tid (pysam/calignmentfile.c:8208)
  File "pysam/cutils.pyx", line 106, in pysam.cutils.force_bytes 
(pysam/cutils.c:2170)

TypeError: Expected bytes, got unicode

Any help to solve this problem would be highly appreciated!

many thanks
--

Lubos Klucar
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Re: [galaxy-dev] Problems uploading files to galaxy

[Lemley, Rob]

Thanks Peter, that's really helpful. I'm glad we're not the only ones running 
into this.

-Rob

Rob Lemley
Systems Administrator – CIRC
University of Rochester

-Original Message-
From: Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Sent: Tuesday, March 15, 2016 10:34 AM
To: John Chilton 
Cc: Lemley, Rob ; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Problems uploading files to galaxy

On Tue, Mar 15, 2016 at 2:21 PM, John Chilton  wrote:
> If you are running jobs as "the real user" with drmaa (using the chown
> script)  - you will probably want to setup a separate job destination
> using the local runner for upload jobs. The upload tool uses files
> that are created outside of Galaxy and these aren't modeled well.
>
> Does this help?
>
> -John

We found the opposite - if using "the real user", the Galaxy v16.01
would do a chown on the datafiles for DRMAA jobs (good) but also
for local jobs (bad):

https://urldefense.proofpoint.com/v2/url?u=http-3A__dev.list.galaxyproject.org_external-2Dchown-2Dscript-2Dpy-2Dand-2Dthe-2Dlocal-2Djob-2Drunner-2Dtt4668738.html&d=BQIBaQ&c=kbmfwr1Yojg42sGEpaQh5ofMHBeTl9EI2eaqQZhHbOU&r=d-Zn2Sbc-XheRlOYkSFXPupZ8ZmuYq52isQBiI3MBWA&m=rMI9zRSmgepuzJAMtXaa8aFFhpcuYbKx2r_h3aC6wIg&s=IZ8BQgQLJhvOnBc_xzGzMYMVVETGgFUhcBM_tNlMXRE&e=
 

I will reply on that thread now with an update...

Peter
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Re: [galaxy-dev] Problems uploading files to galaxy

[Lemley, Rob]

Hi John,

Thanks for getting back to me.

If I'm understanding the XML files correctly, the upload tool is already 
configured to run as a local job. From job_conf.xml:



where "local" is our local job runner and "upload1" is defined in 
data_source/upload.xml.

-Rob

Rob Lemley
Systems Administrator – CIRC
University of Rochester

-Original Message-
From: John Chilton [mailto:jmchil...@gmail.com] 
Sent: Tuesday, March 15, 2016 10:21 AM
To: Lemley, Rob 
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Problems uploading files to galaxy

If you are running jobs as "the real user" with drmaa (using the chown
script)  - you will probably want to setup a separate job destination
using the local runner for upload jobs. The upload tool uses files
that are created outside of Galaxy and these aren't modeled well.

Does this help?

-John


On Fri, Mar 11, 2016 at 6:45 PM, Lemley, Rob  wrote:
> Hi everyone,
>
> I didn’t see any response to my email below. Does anyone have any thoughts? 
> I'm pretty stuck.
>
> Thanks again,
>
> -Rob
>
> Rob Lemley
> Systems Administrator – CIRC
> University of Rochester
>
> -Original Message-
> From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On 
> Behalf Of Lemley, Rob
> Sent: Monday, March 7, 2016 2:03 PM
> To: galaxy-dev@lists.galaxyproject.org
> Subject: [galaxy-dev] Problems uploading files to galaxy
>
> Hi,
>
> I'm hoping you can help out with a problem we are experiencing uploading 
> files to our own Galaxy instance.
>
> When a user tries to upload a file to Galaxy through their web browser, the 
> job errors out:
>
> Traceback (most recent call last):
>   File "/gpfs/fs1/sfw/cibem_galaxy/app/galaxy/tools/data_source/upload.py", 
> line 430, in 
> __main__()
>   File "/gpfs/fs1/sfw/cibem_galaxy/app/galaxy/tools/data_source/upload.py", 
> line 407, in __main__
> for line in open( sys.argv[3], 'r' ):
> IOError: [Errno 13] Permission denied: 
> '/scratch/XX/XX/galaxy/tmp/tmpSlG2pC'
>
> The permissions on the referenced file:
> -rw---+ 1 rlemley  rlemley  317 Mar  7 13:42 tmpSlG2pC
>
> As the Galaxy daemons run as XX_galaxy, it does not have permission to 
> read the file.
>
> I tried modifying external_chown_script.py so that XX_galaxy has 
> permission to read that file, but that caused problems elsewhere so I backed 
> out the changes.
>
> Any suggestions?
>
> Many thanks,
>
> -Rob
>
>
> Rob Lemley
> Systems Administrator - CIRC
> University of Rochester
>
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Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Bjoern Gruening]

On 15.03.2016 18:11, Léo Biscassi wrote:
Hi, thanks for the considerations in the code, I'll make the changes 
later.
The packages Autodock Vina and MGL Tools works fine!? I saw that tests 
passed with success on Travis.


No, not really. You need to create a .shed.yml file to trigger the tests.
Let's move this discussion to github.

Thanks again!
Bjoern


Cheers,

On Tue, Mar 15, 2016 at 4:50 AM Bjoern Gruening 
mailto:bjoern.gruen...@gmail.com>> wrote:


Saw it! Will review it today, this looks really nice!


On 15.03.2016 08:28, Léo Biscassi wrote:

Hi Bjorn, I've created the pull request [1] in your repository. I
will be grateful if you can assist me with the functional tests
on the docking tool and the final validation of the tool
dependencies.

[1] https://github.com/bgruening/galaxytools/pull/310

Thanks a lot!

Best regards,

On Mon, Mar 14, 2016 at 12:56 PM Léo Biscassi
mailto:leo.bisca...@gmail.com>> wrote:

Hi, thanks for the reply.
About the branch model, ok! I'll follow the model presented.
About the error in planemo functional tests, the problem is
that the content of example output is not the same of output
file of test. This is shown by the command diff performed on
planemo test.
Today, I'll create a pull request in your repository for that
we can fix the problem.
Thank for the helps.

I'm excited about this.

Best regards,



On Thu, Mar 10, 2016 at 5:51 PM Björn Grüning
mailto:bjoern.gruen...@gmail.com>> wrote:



Am 10.03.2016 um 21:30 schrieb Léo Biscassi:
> Hi folks,
> I have make somes alterations on my tools to adjust of
according with
> best pratices of development of tools presented in [1]
[2]. The
> repository of tools was changed for [3].
> I was testing the tool of docking [4] with the command
planemo t, but as
> the algorithm used is heuristic, the output files not
have the same
> content that as output files example and planemo tests
fails. Any
> suggestion to solve this problem?

Is there anything in the file that is the same? Filesize?
Some lines
that are everytime the same (no matter where in the file)?

You could create a PR and I will review it and give you
feedback.
Cheers,
Bjoern


> [1]
>

https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html
> [2] https://planemo.readthedocs.org/en/latest/
> [3] https://github.com/leobiscassi/autodock_vina_tools
> [4]
>

https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking
>
> Att.
>
> On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi
mailto:leo.bisca...@gmail.com>
> >> wrote:
>
> Hi Bjorn, the branch model of ChemicalToolBoX is
the same presented
> in [1]? Could guide me about it?
>
> [1]
https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md
>
> Att.
>
> On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi
mailto:leo.bisca...@gmail.com>
> >> wrote:
>
> Ok, thanks!
>
> Best regards,
>
> On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning
> mailto:bjoern.gruen...@gmail.com>
>>
> wrote:
>
>
>
> Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
> > Hi,
> > Thanks all your attention.
> > Although my project is functional
prototype, its current
> version is able to
> > integrate with projects. In fact, I was
looking for
> projects like
> > ChemicalToolBoX because I would like to
develop my tools
> under project that
> > has more options. In this way,
ChemicalToolBoX is a great
> opportunity for
> > me.
> > Can you update the trello card with my
project? Is it
> necessary for you

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Léo Biscassi]

Hi, thanks for the considerations in the code, I'll make the changes later.
The packages Autodock Vina and MGL Tools works fine!? I saw that tests
passed with success on Travis.

Cheers,

On Tue, Mar 15, 2016 at 4:50 AM Bjoern Gruening 
wrote:

> Saw it! Will review it today, this looks really nice!
>
>
> On 15.03.2016 08:28, Léo Biscassi wrote:
>
> Hi Bjorn, I've created the pull request [1] in your repository. I will be
> grateful if you can assist me with the functional tests on the docking tool
> and the final validation of the tool dependencies.
>
> [1] https://github.com/bgruening/galaxytools/pull/310
>
> Thanks a lot!
>
> Best regards,
>
> On Mon, Mar 14, 2016 at 12:56 PM Léo Biscassi 
> wrote:
>
>> Hi, thanks for the reply.
>> About the branch model, ok! I'll follow the model presented.
>> About the error in planemo functional tests, the problem is that the
>> content of example output is not the same of output file of test. This is
>> shown by the command diff performed on planemo test.
>> Today, I'll create a pull request in your repository for that we can fix
>> the problem.
>> Thank for the helps.
>>
>> I'm excited about this.
>>
>> Best regards,
>>
>>
>>
>> On Thu, Mar 10, 2016 at 5:51 PM Björn Grüning 
>> wrote:
>>
>>>
>>>
>>> Am 10.03.2016 um 21:30 schrieb Léo Biscassi:
>>> > Hi folks,
>>> > I have make somes alterations on my tools to adjust of according with
>>> > best pratices of development of tools presented in [1] [2]. The
>>> > repository of tools was changed for [3].
>>> > I was testing the tool of docking [4] with the command planemo t, but
>>> as
>>> > the algorithm used is heuristic, the output files not have the same
>>> > content that as output files example and planemo tests fails. Any
>>> > suggestion to solve this problem?
>>>
>>> Is there anything in the file that is the same? Filesize? Some lines
>>> that are everytime the same (no matter where in the file)?
>>>
>>> You could create a PR and I will review it and give you feedback.
>>> Cheers,
>>> Bjoern
>>>
>>>
>>> > [1]
>>> >
>>> https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html
>>> > [2] https://planemo.readthedocs.org/en/latest/
>>> > [3] https://github.com/leobiscassi/autodock_vina_tools
>>> > [4]
>>> >
>>> https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking
>>> >
>>> > Att.
>>> >
>>> > On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi >> > > wrote:
>>> >
>>> > Hi Bjorn, the branch model of ChemicalToolBoX is the same presented
>>> > in [1]? Could guide me about it?
>>> >
>>> > [1]
>>> https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md
>>> >
>>> > Att.
>>> >
>>> > On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi <
>>> leo.bisca...@gmail.com
>>> > > wrote:
>>> >
>>> > Ok, thanks!
>>> >
>>> > Best regards,
>>> >
>>> > On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning
>>> > mailto:bjoern.gruen...@gmail.com>>
>>> > wrote:
>>> >
>>> >
>>> >
>>> > Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
>>> > > Hi,
>>> > > Thanks all your attention.
>>> > > Although my project is functional prototype, its current
>>> > version is able to
>>> > > integrate with projects. In fact, I was looking for
>>> > projects like
>>> > > ChemicalToolBoX because I would like to develop my tools
>>> > under project that
>>> > > has more options. In this way, ChemicalToolBoX is a great
>>> > opportunity for
>>> > > me.
>>> > > Can you update the trello card with my project? Is it
>>> > necessary for your
>>> > > organization?
>>> >
>>> > I added you :) So you have all right to modify cards.
>>> > Let me know if you need help with Tool development or git.
>>> >
>>> > This is exciting!
>>> > Cheers,
>>> > Bjoern
>>> >
>>> > > Best regards,
>>> > >
>>> > > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning
>>> > >> bjoern.gruen...@gmail.com>>
>>> > > wrote:
>>> > >
>>> > >>
>>> > >>
>>> > >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi:
>>> > >>> Hi,
>>> > >>>
>>> > >>> I've found this Trello card (
>>> > >>> https://trello.com/c/2eIu6SBa/49-autodock-integration
>>> ).
>>> > Do you have more
>>> > >>> information about it?
>>> > >>
>>> > >> Afaik we can not use his work as it was done for some
>>> > company and he
>>> > >> moved on ... so this is unfortunately no option afaik.
>>> > >>
>>> > >>
>>> > >>
>>> > >>> best,
>>> > >>>
>>> > >>> On Mon, Dec 28, 2015

[galaxy-dev] Tool-install error with yaml file

[Rathert , Philipp , Dr .]

Dear all, 
I want to install a bunch of tools using the install-tools 
function. In my yaml file tool.yml i have specified the url if my docker 
instance wit the ip adress i use in the web browser and the api_key is admin

When i run install-tools tool.yml I get the error below and nothing happens.

I attached my tool.yml file in case the error comes from there.

Anybody has an idea whats wrong?

root@galaxy:/galaxy-central# install-tools tool.yml * Starting PostgreSQL 
9.3 database server [ OK ] starting Galaxy Activating virtualenv at .venv 
Ignoring indexes: https://pypi.python.org/simple 
/galaxy-central/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315:
 
SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name 
Indication) extension to TLS is not available on this platform. This may 
cause the server to present an incorrect TLS certificate, which can cause 
validation failures. For more information, see 
https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning. 
SNIMissingWarning 
/galaxy-central/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120:
 
InsecurePlatformWarning: A true SSLContext object is not available. This 
prevents urllib3 from configuring SSL appropriately and may cause certain 
SSL connections to fail. For more information, see 
https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
 
InsecurePlatformWarning Requirement already up-to-date: pip==8.0.2+gx2 in 
./.venv/lib/python2.7/site-packages Requirement already satisfied 
(use --upgrade to upgrade): bx-python==0.7.3 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) 
Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) 
Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) 
Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) 
Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) 
Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) 
Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) 
Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) 
Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) 
Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) 
Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) 
Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) 
Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) 
Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) 
Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) 
Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) 
Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) 
Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) 
Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) 
Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) 
Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) 
Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) 
Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in 
./.venv/lib/python

Re: [galaxy-dev] external_chown_script.py and the local job runner

[Peter Cock]

On Mon, Jan 25, 2016 at 4:59 PM, Peter Cock  wrote:
> On Mon, Jan 25, 2016 at 4:44 PM, John Chilton  wrote:
>> I think the problem is more that it is configured globally and not
>> per-destination. The real user stuff should all be per-destination and
>> not globally configured - since it should be possible to have like a
>> dedicated cluster for Galaxy jobs that just run jobs normally and a
>> general purpose cluster that submits jobs as the real user for
>> accounting purposes.
>
> Excellent point.
>
>> I have created a WIP pull request to move the configuration of these
>> options in that direction:
>>
>> https://github.com/galaxyproject/galaxy/pull/1573
>>
>> I haven't tested any of the changes in the PR yet - I just wanted to
>> open something to ensure I'd come back and finish things this cycle.
>>
>> It is something that I have wanted to do for a while now - see
>> https://trello.com/c/6w8bples. In general there are a bunch of Galaxy
>> options for jobs that can only be configured in galaxy.ini but that
>> you may wish to have different values for depending on the job
>> destination.
>
> That makes a lot of sense :)
>

Recap: Running jobs on a cluster as the real user can break the
local job runner under Galaxy v16.01. This was a Galaxy bug
due to the external_chown_script setting being used on all job
runners (even when the file owner should have stayed as the
Galaxy Linux account).

John had a pull request to improve this,

https://github.com/galaxyproject/galaxy/pull/1573

This was superseded by the following which has been merged:

https://github.com/galaxyproject/galaxy/pull/1688

I think this means that per-job-runner config will be possible
in the next release, so we can set external_chown_script for
only for DRMAA jobs sent to the cluster.

> We're considering trying an alternative of using SGE with a separate
> queue consisting of just the Galaxy server, as a substitute for the
> local worker - but we won't have a chance to try that till next week.

We are currently doing this on our test Galaxy v16.01 server, but
it does make the cluster integration even more complicated (the
Galaxy server must be both an SGE submit node and also an
SGE worker node, and you need an extra queue just for sending
upload jobs etc to run on the Galaxy server).

Peter
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Re: [galaxy-dev] Problems uploading files to galaxy

[Peter Cock]

On Tue, Mar 15, 2016 at 2:21 PM, John Chilton  wrote:
> If you are running jobs as "the real user" with drmaa (using the chown
> script)  - you will probably want to setup a separate job destination
> using the local runner for upload jobs. The upload tool uses files
> that are created outside of Galaxy and these aren't modeled well.
>
> Does this help?
>
> -John

We found the opposite - if using "the real user", the Galaxy v16.01
would do a chown on the datafiles for DRMAA jobs (good) but also
for local jobs (bad):

http://dev.list.galaxyproject.org/external-chown-script-py-and-the-local-job-runner-tt4668738.html

I will reply on that thread now with an update...

Peter
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Re: [galaxy-dev] Problems uploading files to galaxy

[John Chilton]

If you are running jobs as "the real user" with drmaa (using the chown
script)  - you will probably want to setup a separate job destination
using the local runner for upload jobs. The upload tool uses files
that are created outside of Galaxy and these aren't modeled well.

Does this help?

-John


On Fri, Mar 11, 2016 at 6:45 PM, Lemley, Rob  wrote:
> Hi everyone,
>
> I didn’t see any response to my email below. Does anyone have any thoughts? 
> I'm pretty stuck.
>
> Thanks again,
>
> -Rob
>
> Rob Lemley
> Systems Administrator – CIRC
> University of Rochester
>
> -Original Message-
> From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On 
> Behalf Of Lemley, Rob
> Sent: Monday, March 7, 2016 2:03 PM
> To: galaxy-dev@lists.galaxyproject.org
> Subject: [galaxy-dev] Problems uploading files to galaxy
>
> Hi,
>
> I'm hoping you can help out with a problem we are experiencing uploading 
> files to our own Galaxy instance.
>
> When a user tries to upload a file to Galaxy through their web browser, the 
> job errors out:
>
> Traceback (most recent call last):
>   File "/gpfs/fs1/sfw/cibem_galaxy/app/galaxy/tools/data_source/upload.py", 
> line 430, in 
> __main__()
>   File "/gpfs/fs1/sfw/cibem_galaxy/app/galaxy/tools/data_source/upload.py", 
> line 407, in __main__
> for line in open( sys.argv[3], 'r' ):
> IOError: [Errno 13] Permission denied: 
> '/scratch/XX/XX/galaxy/tmp/tmpSlG2pC'
>
> The permissions on the referenced file:
> -rw---+ 1 rlemley  rlemley  317 Mar  7 13:42 tmpSlG2pC
>
> As the Galaxy daemons run as XX_galaxy, it does not have permission to 
> read the file.
>
> I tried modifying external_chown_script.py so that XX_galaxy has 
> permission to read that file, but that caused problems elsewhere so I backed 
> out the changes.
>
> Any suggestions?
>
> Many thanks,
>
> -Rob
>
>
> Rob Lemley
> Systems Administrator - CIRC
> University of Rochester
>
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Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Bjoern Gruening]

Saw it! Will review it today, this looks really nice!

On 15.03.2016 08:28, Léo Biscassi wrote:
Hi Bjorn, I've created the pull request [1] in your repository. I will 
be grateful if you can assist me with the functional tests on the 
docking tool and the final validation of the tool dependencies.


[1] https://github.com/bgruening/galaxytools/pull/310

Thanks a lot!

Best regards,

On Mon, Mar 14, 2016 at 12:56 PM Léo Biscassi > wrote:


Hi, thanks for the reply.
About the branch model, ok! I'll follow the model presented.
About the error in planemo functional tests, the problem is that
the content of example output is not the same of output file of
test. This is shown by the command diff performed on planemo test.
Today, I'll create a pull request in your repository for that we
can fix the problem.
Thank for the helps.

I'm excited about this.

Best regards,



On Thu, Mar 10, 2016 at 5:51 PM Björn Grüning
mailto:bjoern.gruen...@gmail.com>> wrote:



Am 10.03.2016 um 21:30 schrieb Léo Biscassi:
> Hi folks,
> I have make somes alterations on my tools to adjust of
according with
> best pratices of development of tools presented in [1] [2]. The
> repository of tools was changed for [3].
> I was testing the tool of docking [4] with the command
planemo t, but as
> the algorithm used is heuristic, the output files not have
the same
> content that as output files example and planemo tests
fails. Any
> suggestion to solve this problem?

Is there anything in the file that is the same? Filesize? Some
lines
that are everytime the same (no matter where in the file)?

You could create a PR and I will review it and give you feedback.
Cheers,
Bjoern


> [1]
>

https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html
> [2] https://planemo.readthedocs.org/en/latest/
> [3] https://github.com/leobiscassi/autodock_vina_tools
> [4]
>

https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking
>
> Att.
>
> On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi
mailto:leo.bisca...@gmail.com>
> >> wrote:
>
> Hi Bjorn, the branch model of ChemicalToolBoX is the
same presented
> in [1]? Could guide me about it?
>
> [1]
https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md
>
> Att.
>
> On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi
mailto:leo.bisca...@gmail.com>
> >> wrote:
>
> Ok, thanks!
>
> Best regards,
>
> On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning
> mailto:bjoern.gruen...@gmail.com>
>>
> wrote:
>
>
>
> Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
> > Hi,
> > Thanks all your attention.
> > Although my project is functional prototype,
its current
> version is able to
> > integrate with projects. In fact, I was
looking for
> projects like
> > ChemicalToolBoX because I would like to
develop my tools
> under project that
> > has more options. In this way, ChemicalToolBoX
is a great
> opportunity for
> > me.
> > Can you update the trello card with my
project? Is it
> necessary for your
> > organization?
>
> I added you :) So you have all right to modify
cards.
> Let me know if you need help with Tool
development or git.
>
> This is exciting!
> Cheers,
> Bjoern
>
> > Best regards,
> >
> > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning
> mailto:bjoern.gruen...@gmail.com>
>>
> > wrote:
> >
> >>
> >>
> >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi:
> >>> Hi,
> >>>
> >>> I've found this Trello card (

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Léo Biscassi]

Hi Bjorn, I've created the pull request [1] in your repository. I will be
grateful if you can assist me with the functional tests on the docking tool
and the final validation of the tool dependencies.

[1] https://github.com/bgruening/galaxytools/pull/310

Thanks a lot!

Best regards,

On Mon, Mar 14, 2016 at 12:56 PM Léo Biscassi 
wrote:

> Hi, thanks for the reply.
> About the branch model, ok! I'll follow the model presented.
> About the error in planemo functional tests, the problem is that the
> content of example output is not the same of output file of test. This is
> shown by the command diff performed on planemo test.
> Today, I'll create a pull request in your repository for that we can fix
> the problem.
> Thank for the helps.
>
> I'm excited about this.
>
> Best regards,
>
>
>
> On Thu, Mar 10, 2016 at 5:51 PM Björn Grüning 
> wrote:
>
>>
>>
>> Am 10.03.2016 um 21:30 schrieb Léo Biscassi:
>> > Hi folks,
>> > I have make somes alterations on my tools to adjust of according with
>> > best pratices of development of tools presented in [1] [2]. The
>> > repository of tools was changed for [3].
>> > I was testing the tool of docking [4] with the command planemo t, but as
>> > the algorithm used is heuristic, the output files not have the same
>> > content that as output files example and planemo tests fails. Any
>> > suggestion to solve this problem?
>>
>> Is there anything in the file that is the same? Filesize? Some lines
>> that are everytime the same (no matter where in the file)?
>>
>> You could create a PR and I will review it and give you feedback.
>> Cheers,
>> Bjoern
>>
>>
>> > [1]
>> >
>> https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html
>> > [2] https://planemo.readthedocs.org/en/latest/
>> > [3] https://github.com/leobiscassi/autodock_vina_tools
>> > [4]
>> >
>> https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking
>> >
>> > Att.
>> >
>> > On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi > > > wrote:
>> >
>> > Hi Bjorn, the branch model of ChemicalToolBoX is the same presented
>> > in [1]? Could guide me about it?
>> >
>> > [1]
>> https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md
>> >
>> > Att.
>> >
>> > On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi <
>> leo.bisca...@gmail.com
>> > > wrote:
>> >
>> > Ok, thanks!
>> >
>> > Best regards,
>> >
>> > On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning
>> > mailto:bjoern.gruen...@gmail.com>>
>> > wrote:
>> >
>> >
>> >
>> > Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
>> > > Hi,
>> > > Thanks all your attention.
>> > > Although my project is functional prototype, its current
>> > version is able to
>> > > integrate with projects. In fact, I was looking for
>> > projects like
>> > > ChemicalToolBoX because I would like to develop my tools
>> > under project that
>> > > has more options. In this way, ChemicalToolBoX is a great
>> > opportunity for
>> > > me.
>> > > Can you update the trello card with my project? Is it
>> > necessary for your
>> > > organization?
>> >
>> > I added you :) So you have all right to modify cards.
>> > Let me know if you need help with Tool development or git.
>> >
>> > This is exciting!
>> > Cheers,
>> > Bjoern
>> >
>> > > Best regards,
>> > >
>> > > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning
>> > > bjoern.gruen...@gmail.com>>
>> > > wrote:
>> > >
>> > >>
>> > >>
>> > >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi:
>> > >>> Hi,
>> > >>>
>> > >>> I've found this Trello card (
>> > >>> https://trello.com/c/2eIu6SBa/49-autodock-integration).
>> > Do you have more
>> > >>> information about it?
>> > >>
>> > >> Afaik we can not use his work as it was done for some
>> > company and he
>> > >> moved on ... so this is unfortunately no option afaik.
>> > >>
>> > >>
>> > >>
>> > >>> best,
>> > >>>
>> > >>> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning
>> > > bjoern.gruen...@gmail.com>
>> > >>>
>> > >>> wrote:
>> > >>>
>> >  Hi,
>> > 
>> >  yes we had some idea, but nothing materialised so far.
>> > We started with
>> >  the visualisation, because this was more fun :)
>> > 
>> >  Have a look at this board for more ideas:
>> >  https://trello.com/b/t9Wr