Re: [galaxy-dev] Problem upgrading

[Will Holtz]

And as for "sudo git checkout v16.04" not working, it appears to me that
the release commits have not been given tags since v15.07.

-Will

On Fri, May 20, 2016 at 11:52 AM, Scott Szakonyi 
wrote:

> Will, thank you so much! That absolutely did the trick.
>
> -Scott
>
> On Fri, May 20, 2016 at 2:48 PM, Will Holtz  wrote:
>
>> There is a 'git' missing in there. Try:
>> sudo git checkout master && git pull --ff-only origin master
>>
>> -Will
>>
>>
>> On Fri, May 20, 2016 at 11:42 AM, Scott Szakonyi <
>> scott.b.szakony...@nd.edu> wrote:
>>
>>> Hello,
>>>
>>> I'm currently running Galaxy 16.01, and I'd like to upgrade to 16.04.
>>> However, when I attempt to do so, I get an error, and git log shows I'm
>>> still on 16.01.
>>>
>>> $ sudo git checkout master && pull --ff-only origin master
>>> M tool-data/all_fasta.loc.sample
>>> Already on 'master'
>>> -bash: pull: command not found
>>>
>>>
>>> I also tried updating to the exact version:
>>>
>>> sudo git checkout v16.04
>>> error: pathspec 'v16.04' did not match any file(s) known to git.
>>>
>>>
>>> For the record, I'm using Git 1.7.1. I took my commands directory from
>>> the announcement page at
>>> https://docs.galaxyproject.org/en/master/releases/16.04_announce.html
>>>
>>> Any suggestions for ways to get the 16.04 code are greatly appreciated!
>>>
>>> Best,
>>>
>>> --
>>> Scott B. Szakonyi
>>> Research Programmer
>>>
>>> *Center for Research Computing*
>>> 107 Information Technology Center
>>> Notre Dame, IN 46556
>>> http://crc.nd.edu
>>>
>>> ___
>>> 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/
>>>
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>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>>
>> --
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>
>
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
>



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Re: [galaxy-dev] Problem upgrading

[Will Holtz]

There is a 'git' missing in there. Try:
sudo git checkout master && git pull --ff-only origin master

-Will


On Fri, May 20, 2016 at 11:42 AM, Scott Szakonyi 
wrote:

> Hello,
>
> I'm currently running Galaxy 16.01, and I'd like to upgrade to 16.04.
> However, when I attempt to do so, I get an error, and git log shows I'm
> still on 16.01.
>
> $ sudo git checkout master && pull --ff-only origin master
> M tool-data/all_fasta.loc.sample
> Already on 'master'
> -bash: pull: command not found
>
>
> I also tried updating to the exact version:
>
> sudo git checkout v16.04
> error: pathspec 'v16.04' did not match any file(s) known to git.
>
>
> For the record, I'm using Git 1.7.1. I took my commands directory from the
> announcement page at
> https://docs.galaxyproject.org/en/master/releases/16.04_announce.html
>
> Any suggestions for ways to get the 16.04 code are greatly appreciated!
>
> Best,
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
>
> ___
> 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/
>
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>   http://galaxyproject.org/search/mailinglists/
>



-- 
The information contained in this e-mail message or any attachment(s) may
be confidential and/or privileged and is intended for use only by the
individual(s) to whom this message is addressed.  If you are not the
intended recipient, any dissemination, distribution, copying, or use is
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[galaxy-dev] Problem upgrading

[Scott Szakonyi]

Hello,

I'm currently running Galaxy 16.01, and I'd like to upgrade to 16.04.
However, when I attempt to do so, I get an error, and git log shows I'm
still on 16.01.

$ sudo git checkout master && pull --ff-only origin master
M tool-data/all_fasta.loc.sample
Already on 'master'
-bash: pull: command not found


I also tried updating to the exact version:

sudo git checkout v16.04
error: pathspec 'v16.04' did not match any file(s) known to git.


For the record, I'm using Git 1.7.1. I took my commands directory from the
announcement page at
https://docs.galaxyproject.org/en/master/releases/16.04_announce.html

Any suggestions for ways to get the 16.04 code are greatly appreciated!

Best,

-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
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Re: [galaxy-dev] STACKS error

[Geert Vandeweyer]

Hi Yvan,

We had this issue as well, and fixed it for now by adding the 
checkers.py from an old galaxy server. I've added it in attachment if 
you don't have it anymore.


put it in "galaxy-dist/lib/galaxy/datatypes/checkers.py"

If relevant, I also made a few changes to the stacks script itself, but 
I can't remember if is was related (I think due to ordereddict module in 
different python versions)


diff -r 0e0ff9e9c761 stacks.py
--- a/stacks.py Mon Sep 28 13:21:35 2015 +
+++ b/stacks.py Fri May 20 17:53:56 2016 +0200
@@ -14,6 +14,8 @@
 import os, sys, re, shutil
 import glob
 import collections
+import ordereddict
+from ordereddict import OrderedDict
 import gzip, zipfile, tarfile
 import subprocess
 from galaxy.datatypes.checkers import *
@@ -31,7 +33,8 @@
 """
 def galaxy_config_to_tabfiles(input_config):

-   tab_files=collections.OrderedDict()
+   #tab_files=collections.OrderedDict()
+   tab_files=OrderedDict()
for line in open(input_config, "r").readlines():
if line.strip() != '':
extract=line.strip().split("::")
@@ -43,7 +46,8 @@

 def galaxy_config_to_tabfiles_for_STACKS(input_config):

-   tab_files=collections.OrderedDict()
+   #tab_files=collections.OrderedDict()
+tab_files=OrderedDict()
for line in open(input_config, "r").readlines():
if line.strip() != '':
extract=line.strip().split("::")


On 2016-05-20 17:28, Yvan Le Bras wrote:

Thank you John for the rapid answer and the PR!

I have had the same issue trying installing and use a Galaxy-M 
instance 
(https://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0115-8) 
. I cc Ralf concerning this.


Cheers,

Yvan



*De: *"John Chilton" 
*À: *"Yvan Le Bras" 
*Cc: *"Amogelang Raphenya" ,
galaxy-dev@lists.galaxyproject.org
*Envoyé: *Vendredi 20 Mai 2016 17:15:19
*Objet: *Re: [galaxy-dev] STACKS error

This is one the reasons (though not the only one) I generally
discourage putting datatypes in the tool shed - Galaxy isn't very
clear about what interface it provides to datatypes and it would seem
very difficult from my perspective to maintain that interface and grow
Galaxy at the same time.

This checkers module though is clearly useful to datatypes and it is
quite trivial to provide backward compatibility so I've opened a PR to
the new 16.04 release to restore this module -
https://github.com/galaxyproject/galaxy/pull/2389.

Sorry for the inconvenience.

-John


On Fri, May 20, 2016 at 10:45 AM, Yvan Le Bras
 wrote:
> Hi Amos,
>
> Thanks to use Stacks on Galaxy! I already seen this error. This
is due, I
> think, to newest Galaxy versions who don't have the checkers.py
anymore on
> the datatypes folder Thios can be fixed using an older
Galaxy version...
> Otherwise, we are working on a new version of the Stacks Galaxy
tools... who
> will be usable in the upcoming days or not ;)
>
> Cheers,
>
> Yvan
>
>
> 
>
> De: "Amogelang Raphenya" 
> À: galaxy-dev@lists.galaxyproject.org
> Envoyé: Vendredi 20 Mai 2016 16:37:04
> Objet: [galaxy-dev] STACKS error
>
>
> Anyone encountered this error?
>
> Fatal error: Exit code 1 (Error in Stacks Process radtag execution)
> Traceback (most recent call last):
>   File
>

"/galaxylab/production/new/shed_tools/toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/STACKS_procrad.py",
> line 16, in 
> from stacks import *
>   File
>

"/galaxylab/production/new/shed_tools/toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/stacks.py",
> line 19, in 
> from galaxy.datatypes.checkers import *
> ImportError: No module named checkers
>
>
> Cheers.
>
>
> Amos Raphenya, B.Eng
> Bioinformatics Software Developer
> Department of Biochemistry & Biomedical Sciences
> McMaster University, MDCL 2317
> p: (905) 525-9140
> a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1
> e:  raphe...@mcmaster.ca
> skype: amos_raphenya
>
>
> ___
> 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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>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
>
>
>
> --
>

Re: [galaxy-dev] Error when executing cleanup scripts

[Scott Szakonyi]

Hi Dannon,

That absolutely did the trick. Thanks so much for your assistance.

Best,

Scott

On Fri, May 20, 2016 at 9:11 AM, Dannon Baker 
wrote:

> Hi Scott,
>
> The quick fix is to source your virtualenv first and you should be good to
> go.
>
> -Dannon
>
> On Fri, May 20, 2016 at 9:07 AM Scott Szakonyi 
> wrote:
>
>> Hi all,
>>
>> I'm getting an error when executing the cleanup scripts in Galaxy 16.01.
>> It appears the script is unable to import sqlalchemy, but my understanding
>> is that Galaxy can't function without it, so I'm at a loss to explain.
>> Here's the error I'm getting:
>>
>> $ sh scripts/cleanup_datasets/delete_userless_histories.sh
>> Traceback (most recent call last):
>>   File "./scripts/cleanup_datasets/cleanup_datasets.py", line 13, in
>> 
>> import sqlalchemy as sa
>> ImportError: No module named sqlalchemy
>>
>>
>> We have relatively limited space on our storage server, so it's
>> imperative that I be able to execute these scripts and be able to clean up
>> deleted material. I welcome any suggestions.
>>
>> Best regards,
>>
>> --
>> Scott B. Szakonyi
>> Research Programmer
>>
>> *Center for Research Computing*
>> 107 Information Technology Center
>> Notre Dame, IN 46556
>> http://crc.nd.edu
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>
>


-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
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Re: [galaxy-dev] STACKS error

[Yvan Le Bras]

Hi Amos, 

Thanks to use Stacks on Galaxy! I already seen this error. This is due, I 
think, to newest Galaxy versions who don't have the checkers.py anymore on the 
datatypes folder Thios can be fixed using an older Galaxy version... 
Otherwise, we are working on a new version of the Stacks Galaxy tools... who 
will be usable in the upcoming days or not ;) 

Cheers, 

Yvan 

- Mail original -

> De: "Amogelang Raphenya" 
> À: galaxy-dev@lists.galaxyproject.org
> Envoyé: Vendredi 20 Mai 2016 16:37:04
> Objet: [galaxy-dev] STACKS error

> Anyone encountered this error?

> Fatal error: Exit code 1 (Error in Stacks Process radtag execution)
> Traceback (most recent call last):
> File "/galaxylab/production/new/shed_tools/
> toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/STACKS_procrad.py
> ", line 16, in 
> from stacks import *
> File "/galaxylab/production/new/shed_tools/
> toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/stacks.py
> ", line 19, in 
> from galaxy.datatypes.checkers import *
> ImportError: No module named checkers

> Cheers.

> Amos Raphenya, B.Eng
> Bioinformatics Software Developer
> Department of Biochemistry & Biomedical Sciences
> McMaster University, MDCL 2317
> p: (905) 525-9140
> a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1
> e: raphe...@mcmaster.ca
> skype: amos_raphenya

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

> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
-- 
-
 
Yvan Le Bras, PhD @Yvan2935 <°>< 
e-Biogenouest project http://www.e-biogenouest.org 
CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042 Rennes Cedex 
tél.: +33 (0) 2 99 84 71 79 / +33 (0) 6.10.43.96.51 
yvan.le_b...@irisa.fr 
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[galaxy-dev] STACKS error

[Raphenya, Amogelang]

Anyone encountered this error?



Fatal error: Exit code 1 (Error in Stacks Process radtag execution)
Traceback (most recent call last):
  File "/galaxylab/production/new/shed_tools/toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/STACKS_procrad.py", line 16, in 
from stacks import *
  File "/galaxylab/production/new/shed_tools/toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/stacks.py", line 19, in 
from galaxy.datatypes.checkers import *
ImportError: No module named checkers


Cheers.






Amos Raphenya, B.Eng 

Bioinformatics Software Developer

Department of Biochemistry & Biomedical Sciences

McMaster University, MDCL 2317

p: (905) 525-9140

a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1

e:  raphe...@mcmaster.ca

skype: amos_raphenya



















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Re: [galaxy-dev] Error when executing cleanup scripts

[Dannon Baker]

Hi Scott,

The quick fix is to source your virtualenv first and you should be good to
go.

-Dannon

On Fri, May 20, 2016 at 9:07 AM Scott Szakonyi 
wrote:

> Hi all,
>
> I'm getting an error when executing the cleanup scripts in Galaxy 16.01.
> It appears the script is unable to import sqlalchemy, but my understanding
> is that Galaxy can't function without it, so I'm at a loss to explain.
> Here's the error I'm getting:
>
> $ sh scripts/cleanup_datasets/delete_userless_histories.sh
> Traceback (most recent call last):
>   File "./scripts/cleanup_datasets/cleanup_datasets.py", line 13, in
> 
> import sqlalchemy as sa
> ImportError: No module named sqlalchemy
>
>
> We have relatively limited space on our storage server, so it's imperative
> that I be able to execute these scripts and be able to clean up deleted
> material. I welcome any suggestions.
>
> Best regards,
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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[galaxy-dev] Error when executing cleanup scripts

[Scott Szakonyi]

Hi all,

I'm getting an error when executing the cleanup scripts in Galaxy 16.01. It
appears the script is unable to import sqlalchemy, but my understanding is
that Galaxy can't function without it, so I'm at a loss to explain. Here's
the error I'm getting:

$ sh scripts/cleanup_datasets/delete_userless_histories.sh
Traceback (most recent call last):
  File "./scripts/cleanup_datasets/cleanup_datasets.py", line 13, in

import sqlalchemy as sa
ImportError: No module named sqlalchemy


We have relatively limited space on our storage server, so it's imperative
that I be able to execute these scripts and be able to clean up deleted
material. I welcome any suggestions.

Best regards,

-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
___
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Re: [galaxy-dev] not sure what I can do about this...

[Marius van den Beek]

Hi Edgar,

it’s a good idea to use python2.7 for galaxy, since 16.01 is the last
release supporting python 2.6.
In general you can create a new virrtualenv with a a specific python
interpreter like this:

virtualenv -p  

If you create a new new virtualenv .venv in your galaxy source folder,
run.sh will pick this up.
If you are using a different way to start galaxy, you can use something
along the lines of

/scripts/paster.py
serve config/galaxy.ini>

Hope that will get you past the problems starting up galaxy.

Cheers,
Marius
​

On 19 May 2016 at 14:48, Fernandez Edgar 
wrote:

> Hey Guys,
>
>
>
> I’ve fixed my first problem with the environment.
>
> But I’m still getting the second one.
>
>
>
> Also, did any of you guys try to deploy galaxy with Microsoft Azure?
>
> I’m actually looking into it and I was wondering if you had any input…
>
>
>
> Let me know if you have any info on my libchtslib.so: input error or
> Microsoft Azure.
>
>
>
> Cheers!
>
>
>
> *Edgar Fernandez*
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la Communication
>
> *Université de Montréal*
>
>
>
> PAVILLON ROGER-GAUDRY, bureau X-210
>
> (  Bur. : *1-514-343-6111 poste 16568*
>
>
>
>
>
> *From:* Fernandez Edgar
> *Sent:* May-18-16 2:00 PM
> *To:* galaxy-...@bx.psu.edu
> *Subject:* RE: [galaxy-dev] not sure what I can do about this...
>
>
>
> Hey Guys,
>
>
>
> Hope everyone is doing well.
>
>
>
> So I’m back at galaxy v16.01
>
>
>
> I’m having a small problem.
>
> My python system version is 2.6.6
>
>
>
> So I installed python version 2.7.8 from  Software Collection Library
> release 1.2 packages for Oracle Linux 6 (x86_64)
> 
>
> This means I need to source an environment before being about to use it.
>
> So what I’ve created a file config/local_env.sh with:
>
> *# Source python27*
>
> *export PATH=/opt/rh/python27/root/usr/bin${PATH:+:${PATH}}*
>
> *export
> LD_LIBRARY_PATH=/opt/rh/python27/root/usr/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}*
>
> *export MANPATH=/opt/rh/python27/root/usr/share/man:${MANPATH}*
>
> *# For systemtap*
>
> *export
> XDG_DATA_DIRS=/opt/rh/python27/root/usr/share${XDG_DATA_DIRS:+:${XDG_DATA_DIRS}}*
>
> *# For pkg-config*
>
> *export
> PKG_CONFIG_PATH=/opt/rh/python27/root/usr/lib64/pkgconfig${PKG_CONFIG_PATH:+:${PKG_CONFIG_PATH}}*
>
>
>
> These export comes directly with the installation of python 2.7.8 in the
> file /opt/rh/python27/enable.
>
> But when I started my galaxy it didn’t stick.
>
>
>
> I had to insert those exports into the file run.sh right before the
> following line:
>
> *./scripts/common_startup.sh $common_startup_args || exit 1*
>
>
>
> Any suggestions to make it work?
>
>
>
> Also, I get this error :
>
> *Traceback (most recent call last):*
>
> *  File "./scripts/paster.py", line 27, in *
>
> *serve.run()*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py",
> line 1061, in run*
>
> *invoke(command, command_name, options, args[1:])*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py",
> line 1067, in invoke*
>
> *exit_code = runner.run(args)*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py",
> line 223, in run*
>
> *result = self.command()*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py",
> line 639, in command*
>
> *app = loadapp( app_spec, name=app_name, relative_to=base,
> global_conf=vars)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line
> 295, in loadapp*
>
> *return loadobj(APP, uri, name=name, **kw)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line
> 319, in loadobj*
>
> *global_conf=global_conf)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line
> 344, in loadcontext*
>
> *global_conf=global_conf)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line
> 368, in _loadconfig*
>
> *return loader.get_context(object_type, name, global_conf)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line
> 506, in get_context*
>
> *section)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line
> 565, in _context_from_explicit*
>
> *value = import_string(found_expr)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", line
> 125, in import_string*
>
> *return pkg_resources.EntryPoint.parse("x=" + s).load(False)*
>
> *  File
> "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pkg_resources.py",
> line 2260, in load*
>
> *entry = __import__(self.module_name, globals(),globals(),
> ['__name__'])*
>
> *  File "/home/galaxy/galaxy-v16.01/lib/galaxy/web/buildapp.py", line 5,
> in *
>
> *from galaxy.webapps.galaxy.buildapp