Re: [galaxy-dev] example_watch_folder.py : URL did not return JSON data
It should be set on line 29 as the result of that submit function. Can you
add (between 29 and 30) a 'print library' to see what that call actually
results in?
Off the top of my head, this might be happening if your user account (that
the API key is associated with) isn't an admin account -- only admins can
create Data Libraries.
On Tue, Mar 12, 2013 at 6:35 PM, Rob Leclerc robert.lecl...@gmail.comwrote:
Hi Dannon. Thanks! I had been experimenting with BioBlend and forgot to
add the /api/ on the url.
./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f
http://localhost:8080/api/ /Users/Rob/Documents/galaxy-db/input/
/Users/Rob/Documents/galaxy-db/output/ API Imports 2a56795cad3c7db3
However, I am now running into a new error when it tries to create the API
Imports folder
Traceback (most recent call last):
File ./example_watch_folder.py, line 87, in module
main(api_key, api_url, in_folder, out_folder, data_library, workflow )
File ./example_watch_folder.py, line 30, in main
library_id = library[0]['id']
KeyError: 0
(This is coming from the section that creates 'API Imports' library if it
doesn't already exist)
24: for library in libs:
25: if library['name'] == data_library:
26: library_id = library['id']
27: if not library_id:
28:lib_create_data = {'name':data_library}
29:library = submit(api_key, api_url + 'libraries', lib_create_data,
return_formatted=False)
30:library_id = library[0]['id']
As I mentioned, I'm not familiar with python, but I can't see where
'library[0]['id']' is set or is in scope, since this seems to be the item in
the iterator above this section.
Cheers,
Rob
Rob Leclerc, PhD
http://www.linkedin.com/in/robleclerchttps://twitter.com/#!/robleclerc
P: (US) +1-(917)-873-3037
P: (Shanghai) +86-1-(861)-612-5469
Personal Email: rob.lecl...@aya.yale.edu
On Tue, Mar 12, 2013 at 6:14 PM, Dannon Baker dannon.ba...@gmail.comwrote:
The second argument there should point to the url of Galaxy's API --
in this case http://localhost:8080/api, I'm guessing.
-Dannon
On Tue, Mar 12, 2013 at 6:11 PM, Rob Leclerc robert.lecl...@gmail.com
wrote:
I'm trying to get the example_watch_folder.py to work with a simple
example,
but I am running into an error (Caveat, python is not my native
language)
I call the following script, but get the subsequent error:
$ ./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f
http://localhost:8080/ /Users/Rob/Documents/galaxy-db/input/
/Users/Rob/Documents/galaxy-db/output/ API Imports 2a56795cad3c7db3
URL did not return JSON data
The preconditions I have in place are:
1. I copied my api_key: 8c25bc83f6f9e4001dd21eb7b64f063f
2. I created a new history on http://localhost:8080
3. I downloaded the the exons from hg19/chr22 from UCSC
3. On the dataset I performed a Text Manipulation Select first (20
lines)
4. I extracted a workflow from the history and recorded the workflow id
(2a56795cad3c7db3).
5. I created directories:
/Users/Rob/Documents/galaxy-db/input/
/Users/Rob/Documents/galaxy-db/output/
My args may be malformed. Can someone provide me an example of a theirs?
Cheers,
Rob
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Re: [galaxy-dev] Galaxy on Cluster - how to set -a flag with username
Hi guys, I just wanted to check in and see if anyone had any ideas on this. (It's actually the -A flag I'm after.) I did try putting this in universe.wsgi: default_cluster_job_runner = drmaa://-V -pe batch 8 -A Account_Name/ I was thinking galaxy might substitute the user name for Account_Name but no luck :-( -Greg On Tue, Mar 12, 2013 at 1:42 PM, greg margeem...@gmail.com wrote: In our local galaxy install we want the cluster jobs to be run from the galaxy user but we want to include a -a [account name] to our grid software bills properly. Here's what I currently have in universe.wsgi: default_cluster_job_runner = drmaa://-V -pe batch 8/ What I want is something like this: default_cluster_job_runner = drmaa://-V -pe batch 8 -a [logged in user name]/ Is this possible? Thanks, Greg ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] example_watch_folder.py : URL did not return JSON data
Hi Dannon,
Thanks. I've moved to a full size monitor, apparently my eyes are going!
They *key error: 0* seems to be the result of a bug in the code.
print(library)
results in:
{'url': '/api/libraries/4b187121143038ff', 'id': '4b187121143038ff',
'name': 'API Import11'}
So library[0]['id'] doesn't point to anything, resulting in the key error.
I changed the code on line 30
library_id = library['id']
This seems to fix the issue. I've now got to the section of code where I am
watching the in_folder, but there doesn't seem to be any subsequent
activity. I'll post my findings or questions as I make progress or lack
thereof.
Cheers,
Rob
On Wed, Mar 13, 2013 at 7:35 AM, Dannon Baker dannon.ba...@gmail.comwrote:
It should be set on line 29 as the result of that submit function. Can
you add (between 29 and 30) a 'print library' to see what that call
actually results in?
Off the top of my head, this might be happening if your user account (that
the API key is associated with) isn't an admin account -- only admins can
create Data Libraries.
On Tue, Mar 12, 2013 at 6:35 PM, Rob Leclerc robert.lecl...@gmail.comwrote:
Hi Dannon. Thanks! I had been experimenting with BioBlend and forgot to
add the /api/ on the url.
./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f
http://localhost:8080/api/ /Users/Rob/Documents/galaxy-db/input/
/Users/Rob/Documents/galaxy-db/output/ API Imports 2a56795cad3c7db3
However, I am now running into a new error when it tries to create the
API Imports folder
Traceback (most recent call last):
File ./example_watch_folder.py, line 87, in module
main(api_key, api_url, in_folder, out_folder, data_library, workflow )
File ./example_watch_folder.py, line 30, in main
library_id = library[0]['id']
KeyError: 0
(This is coming from the section that creates 'API Imports' library if it
doesn't already exist)
24: for library in libs:
25: if library['name'] == data_library:
26: library_id = library['id']
27: if not library_id:
28:lib_create_data = {'name':data_library}
29:library = submit(api_key, api_url + 'libraries', lib_create_data,
return_formatted=False)
30:library_id = library[0]['id']
As I mentioned, I'm not familiar with python, but I can't see where
'library[0]['id']' is set or is in scope, since this seems to be the item in
the iterator above this section.
Cheers,
Rob
On Tue, Mar 12, 2013 at 6:14 PM, Dannon Baker dannon.ba...@gmail.comwrote:
The second argument there should point to the url of Galaxy's API --
in this case http://localhost:8080/api, I'm guessing.
-Dannon
On Tue, Mar 12, 2013 at 6:11 PM, Rob Leclerc robert.lecl...@gmail.com
wrote:
I'm trying to get the example_watch_folder.py to work with a simple
example,
but I am running into an error (Caveat, python is not my native
language)
I call the following script, but get the subsequent error:
$ ./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f
http://localhost:8080/ /Users/Rob/Documents/galaxy-db/input/
/Users/Rob/Documents/galaxy-db/output/ API Imports 2a56795cad3c7db3
URL did not return JSON data
The preconditions I have in place are:
1. I copied my api_key: 8c25bc83f6f9e4001dd21eb7b64f063f
2. I created a new history on http://localhost:8080
3. I downloaded the the exons from hg19/chr22 from UCSC
3. On the dataset I performed a Text Manipulation Select first (20
lines)
4. I extracted a workflow from the history and recorded the workflow id
(2a56795cad3c7db3).
5. I created directories:
/Users/Rob/Documents/galaxy-db/input/
/Users/Rob/Documents/galaxy-db/output/
My args may be malformed. Can someone provide me an example of a
theirs?
Cheers,
Rob
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and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
___
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and other Galaxy lists, please use the interface at:
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[galaxy-dev] Error during registration phase
Hello, I'm trying to register me as a user in the galaxy-es. I installed galaxy-es locally and always I try to register a user I have the error message: Error during registration phase. Please contact the administrator Thanks Ramão Tiago Tiburski ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Some problems setting up a new cloudman instance on AWS
Dannon, Thanks again for the response. I tried this and it was not successful. (same error) I am pretty much running CloudMan out of the box, plus one update, plus a few minor config file changes (already described in my first post.) The only thing I did that was different from the documentation is when I initiated SSH, it asked me if I wanted to configure NX client. I said yes and this process executed successfully. I am rapidly reaching the end of my time allocation to spend on this. Do you know of anyone who would be willing to do a couple of hours of paid work to setup and configure a cloud based Galaxy for our use? Thanks, Adam On 3/8/13 5:41 PM, Dannon Baker dannon.ba...@gmail.com wrote: This is probably due to the version of your cloud galaxy installation being slightly older than the currently deployed tool shed version. If you use the cloud admin panel to update to a more recent galaxy-dist (or just do it yourself after ssh'ing in), this should be resolved. -Dannon ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] example_watch_folder.py : URL did not return JSON data
I was able to get the script to work. I've written down some notes for a
quickstart for anyone else who might be following in my footsteps.
1. Create input and output directores where you will drop and emit files.
In my example I used:
/Users/Rob/Documents/galaxy-drop/input
/Users/Rob/Documents/galaxy-drop/output
2. Edit the galaxy-dist configuration script (universe_wsgi.ini) and set:
allow_library_path_paste = true
3. In example_watch_folder.py, comment out line 30 and replace it with:
#library_id = library[0]['id] This causes a key error : 0
library_id = library['id']
4. CREATE A SAMPLE Workflow Dataset:
1. Start Galaxy
2. Go to USCS and upload the Exons from chr22 to your clean history file
3. Use the Text Manipulation tool to select the first 5 lines of the
gene exon file
4. Extract the workflow
5. *RESTART Galaxy* (You'll get a 500 Internal Server Error if you try
to run this without restarting)
6. Download the exons file to local
5. In your browser go to: http://localhost:8080/api/workflows and identify
the id of the workflow you've just created. Let's assume it is
(4b187121143038ff) and that your api_key for admin is
(8c25bc83f6f9e4001dd21eb7b64f063f)
6. Run the script:
./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f
http://localhost:8080/api/ /Users/Rob/Documents/galaxy-drop/input
/Users/Rob/Documents/galaxy-drop/output My API Import 4b187121143038ff
7. Copy the exons file to /Users/Rob/Documents/galaxy-drop/input when the
process is complete the file will be placed in
/Users/Rob/Documents/galaxy-drop/output
8. In your browser go to: http://localhost:8080/api/histories locate the
recently created history and then navigate to:
http://localhost:8080/api/histories/history_id/contents
where history_id is the id of the history that was created when you ran
the dataset on the last workflow.
This is my result. The second file is the output file.
[
{
id: 0d16186aaff7cbfd,
name: Galaxy1-[Exons_chr22].bed,
type: file,
url: /api/histories/2d9035b3fc152403/contents/0d16186aaff7cbfd
},
{
id: 81991b32733a4fc4,
name: top200,
type: file,
url: /api/histories/2d9035b3fc152403/contents/81991b32733a4fc4
]
9. You can navigate to the JSON description of the file in your browser:
http://localhost:8080/api/histories/2d9035b3fc152403/contents/81991b32733a4fc4
and the output file can be downloaded here:
http:localhost:8080/datasets/81991b32733a4fc4/display?to_ext=data
Cheers!
Rob
On Wed, Mar 13, 2013 at 12:15 PM, Rob Leclerc robert.lecl...@gmail.comwrote:
Hi Dannon,
Thanks. I've moved to a full size monitor, apparently my eyes are going!
They *key error: 0* seems to be the result of a bug in the code.
print(library)
results in:
{'url': '/api/libraries/4b187121143038ff', 'id': '4b187121143038ff',
'name': 'API Import11'}
So library[0]['id'] doesn't point to anything, resulting in the key error.
I changed the code on line 30
library_id = library['id']
This seems to fix the issue. I've now got to the section of code where I
am watching the in_folder, but there doesn't seem to be any subsequent
activity. I'll post my findings or questions as I make progress or lack
thereof.
Cheers,
Rob
On Wed, Mar 13, 2013 at 7:35 AM, Dannon Baker dannon.ba...@gmail.comwrote:
It should be set on line 29 as the result of that submit function. Can
you add (between 29 and 30) a 'print library' to see what that call
actually results in?
Off the top of my head, this might be happening if your user account
(that the API key is associated with) isn't an admin account -- only admins
can create Data Libraries.
On Tue, Mar 12, 2013 at 6:35 PM, Rob Leclerc robert.lecl...@gmail.comwrote:
Hi Dannon. Thanks! I had been experimenting with BioBlend and forgot to
add the /api/ on the url.
./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f
http://localhost:8080/api/ /Users/Rob/Documents/galaxy-db/input/
/Users/Rob/Documents/galaxy-db/output/ API Imports 2a56795cad3c7db3
However, I am now running into a new error when it tries to create the
API Imports folder
Traceback (most recent call last):
File ./example_watch_folder.py, line 87, in module
main(api_key, api_url, in_folder, out_folder, data_library, workflow
)
File ./example_watch_folder.py, line 30, in main
library_id = library[0]['id']
KeyError: 0
(This is coming from the section that creates 'API Imports' library if
it doesn't already exist)
24: for library in libs:
25: if library['name'] == data_library:
26: library_id = library['id']
27: if not library_id:
28:lib_create_data = {'name':data_library}
29:library = submit(api_key, api_url + 'libraries',
lib_create_data, return_formatted=False)
30:library_id = library[0]['id']
As I mentioned, I'm not familiar with python, but I can't see where
[galaxy-dev] Tool config for accordian-like subpanels?
I have a single tool with several different major modes. Each mode has its own uniques group of options that can be managed separately. Rathan than make five different tools, I would like to put it together and simply have the user interface show just the options for the selected mode. People do this in web pages sometimes using Jquery Accordian tabs. Is there any support to have something like Jquery accordion grouping of options? see that the drill down , but it is only used for setting binary options. Thanks,Ted ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] New Features
Hi Galaxy-Team, Can you please add the AxtToFasta and AxtToConcatenatedFasta Tools, which currently exist and work on PSU Test, onto the main PSU Galaxy Server. Thank you, Gary. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] How to add images/pictures into Galaxy Published Pages?
Hi, I am interested in this too. So how do you do this please? Should I first create an html file outside galaxy and then load that file into Galaxy/history second? Or there is better way to do this? I understood the images need to be somewhere where Galaxy can access and display. Regards, From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Huayan Gao Sent: Tuesday, March 12, 2013 8:02 PM To: Björn Grüning Cc: galaxy-dev@lists.bx.psu.edu List Subject: Re: [galaxy-dev] How to add images/pictures into Galaxy Published Pages? Thanks Bjoern! I figured it out too. I put the pictures in the static/images/Pages folder, then use them in the page. The main idea is to find a place with valid URL to store the pictures first. :-) Best, Huayan On Tue, Mar 12, 2013 at 5:41 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.demailto:bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Huayan, in your page-editor you have a picture symbol. As you mentioned you need to specify a path to an image. For my pages I created a history where I store all my pictures. Afterwards I copy the full URL of that picture to the page. So use galaxy to store you image collection :) Hope that helps, Bjoern Hi, I am trying to create a page in Galaxy and want to add some pictures/ screenshots. So how could I do this? I clicked the image button but it needs a URL not the path from my local computer. Thanks, Huayan ___ 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: http://lists.bx.psu.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: http://lists.bx.psu.edu/
Re: [galaxy-dev] How to add images/pictures into Galaxy Published Pages?
Hi Hakeem, I am interested in this too. So how do you do this please? Should I first create an html file outside galaxy and then load that file into Galaxy/history second? Or there is better way to do this? I understood the images need to be somewhere where Galaxy can access and display. you can simply upload you pictures to galaxy, make your history accessible to everyone and than copy the links from the download-button and paste it into your page. Cheers, Bjoern Thanks Bjoern! I figured it out too. I put the pictures in the static/images/Pages folder, then use them in the page. The main idea is to find a place with valid URL to store the pictures first. :-) Best, Huayan On Tue, Mar 12, 2013 at 5:41 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Huayan, in your page-editor you have a picture symbol. As you mentioned you need to specify a path to an image. For my pages I created a history where I store all my pictures. Afterwards I copy the full URL of that picture to the page. So use galaxy to store you image collection :) Hope that helps, Bjoern Hi, I am trying to create a page in Galaxy and want to add some pictures/ screenshots. So how could I do this? I clicked the image button but it needs a URL not the path from my local computer. Thanks, Huayan ___ 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: http://lists.bx.psu.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: http://lists.bx.psu.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: http://lists.bx.psu.edu/
[galaxy-dev] hg push to remote tool shed fails with abort: authorization failed
Hey y'all, Even through http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Pushing_changes_to_a_repository_using_hg_from_the_command_line shows a working example of a hg push, I have not been able to push changes to a remote toolshed successfull. Here's an example of an unsuccessful attempt:. $ vi README $ hg commit -m 'bla' -u jorrit $ hg push pushing to http://jor...@testtoolshed.g2.bx.psu.edu/repos/jorrit/obotest searching for changes http authorization required realm: user: jorrit password: abort: authorization failed tried this with hg versions: Mercurial Distributed SCM (version 2.4.2+20130102) and Mercurial Distributed SCM (version 2.0.2) Curious to hear how I can get a hg push to remote repo to work from commandline! -jorrit ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Internal Server Error - Creating Workflows
If you create a Workflow and then try to access it through the API, https://main.g2.bx.psu.edu/api/workflows/workflow_id the server will emit a 500 Internal Server Error. Changing the output filename on the workflow and then saving seems to fix the issue. Cheers, Rob ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] hg push to remote tool shed fails with abort: authorization failed
To add some information to my earlier post - It seems that the remote repository is updated, but the commandline returns a confusing abort message. Trying on a private test toolshed, I see the following in the community-webapp.log: 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=capabilities HTTP/1.1 200 130 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=batch HTTP/1.1 200 43 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=branchmap HTTP/1.1 200 48 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=branchmap HTTP/1.1 200 48 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:19 +] GET /repos/testjorrit/testrepo?cmd=listkeys HTTP/1.1 200 - - mercurial/proto-1.0 173.11.123.170 - testjorrit [13/Mar/2013:22:08:23 +] POST /repos/testjorrit/testrepo?cmd=unbundle HTTP/1.1 200 - - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:24 +] GET /repos/testjorrit/testrepo?cmd=listkeys HTTP/1.1 200 58 - mercurial/proto-1.0 173.11.123.170 - - [13/Mar/2013:22:08:24 +] POST /repos/testjorrit/testrepo?cmd=pushkey HTTP/1.1 401 - - mercurial/proto-1.0 Which seems to indicate that most http get/post succeed, but the last one, pushkey, fails to authenticate. I am wondering whether I am the only one seeing this confusing behaviour and what I can do to stop this from happening. thx, -jorrit On Mar 13, 2013, at 2:37 PM, jorrit poelen wrote: Hey y'all, Even through http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Pushing_changes_to_a_repository_using_hg_from_the_command_line shows a working example of a hg push, I have not been able to push changes to a remote toolshed successfull. Here's an example of an unsuccessful attempt:. $ vi README $ hg commit -m 'bla' -u jorrit $ hg push pushing to http://jor...@testtoolshed.g2.bx.psu.edu/repos/jorrit/obotest searching for changes http authorization required realm: user: jorrit password: abort: authorization failed tried this with hg versions: Mercurial Distributed SCM (version 2.4.2+20130102) and Mercurial Distributed SCM (version 2.0.2) Curious to hear how I can get a hg push to remote repo to work from commandline! -jorrit ___ 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: http://lists.bx.psu.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: http://lists.bx.psu.edu/
[galaxy-dev] example_watch_folder.py
If you're having problems with example_watch_folder.py you may need to increase the delay hack on line 55 to 15-20 seconds. Without the increased delay, it would upload a zerobyte file for me. It's not clear why, but there is a delay between the creation of a file name and the setting of the file to the dataset. Cheers, Rob ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Datatype dropdown only 8px wide
Can someone point me to where this fix is... I can't find it anywhere and I am running into this problem as well. - Nik. On Mon, Mar 4, 2013 at 9:54 AM, Kelvin Chan kelvin.c...@seqmatic.comwrote: Nevermind, I noticed that the wiki page on Install galaxy was recently updated to show how to do this. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Kelvin Chan Sent: Monday, March 04, 2013 9:50 AM To: 'Nate Coraor'; 'Björn Grüning' Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Datatype dropdown only 8px wide Hi Nate, I have checked and I am indeed in the Default branch. Is there an easy way to switch over to the stable branch via command line? -Kelvin -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: Monday, March 04, 2013 8:52 AM To: Björn Grüning Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Datatype dropdown only 8px wide All, Could you check whether you are running the default or stable branch of galaxy-dist? You can find out with the `hg branch` command. I believe this problem should only exist if you're running the default (development) branch, which is not recommended. Thanks, --nate On Mar 4, 2013, at 1:17 AM, Björn Grüning wrote: Hi Peter, i think it was fixed in 0ea9f51. You need to adopt static/style/base.less. Cheers, Bjoern I'm seeing something similar with a local galaxy-dist install that was also installed from bitbucket about 1.5-2 weeks ago, however, in my case, the width is set to 6px, e.g. div class=select2-container id=s2id_autogen2 style=width: 6px. In fact, I started seeing this after I upgraded a previous install - and based on this behavior, I did a complete re-install, but am still getting it. Does anyone know whether or not this has been fixed and pushed back to repository so we can pull the fix? On Fri, Mar 1, 2013 at 3:59 PM, Kelvin Chan kelvin.c...@seqmatic.com wrote: Hello, I am having a slight issue with the Datatype tab of the edit page. I am using a locally installed version of galaxy-dist obtained from bitbucket. I cannot see anything in the dropdown menu to change the datatype. According to the HTML, the box is only 8px wide. div class=select2-container id=s2id_autogen2 style=width: 8px Is there any way to fix this problem without having to re-install galaxy? Thanks, Kelvin ___ 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: http://lists.bx.psu.edu/ -- Peter Waltman, Ph.D. pwalt...@ucsc.edu 617.347.1876 ___ 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: http://lists.bx.psu.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: http://lists.bx.psu.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: http://lists.bx.psu.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: http://lists.bx.psu.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: http://lists.bx.psu.edu/ -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Datatype dropdown only 8px wide
P.S. I am not a galaxy developer :) On Wed, Mar 13, 2013 at 6:04 PM, Nikhil Joshi najo...@ucdavis.edu wrote: Can someone point me to where this fix is... I can't find it anywhere and I am running into this problem as well. - Nik. On Mon, Mar 4, 2013 at 9:54 AM, Kelvin Chan kelvin.c...@seqmatic.comwrote: Nevermind, I noticed that the wiki page on Install galaxy was recently updated to show how to do this. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Kelvin Chan Sent: Monday, March 04, 2013 9:50 AM To: 'Nate Coraor'; 'Björn Grüning' Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Datatype dropdown only 8px wide Hi Nate, I have checked and I am indeed in the Default branch. Is there an easy way to switch over to the stable branch via command line? -Kelvin -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: Monday, March 04, 2013 8:52 AM To: Björn Grüning Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Datatype dropdown only 8px wide All, Could you check whether you are running the default or stable branch of galaxy-dist? You can find out with the `hg branch` command. I believe this problem should only exist if you're running the default (development) branch, which is not recommended. Thanks, --nate On Mar 4, 2013, at 1:17 AM, Björn Grüning wrote: Hi Peter, i think it was fixed in 0ea9f51. You need to adopt static/style/base.less. Cheers, Bjoern I'm seeing something similar with a local galaxy-dist install that was also installed from bitbucket about 1.5-2 weeks ago, however, in my case, the width is set to 6px, e.g. div class=select2-container id=s2id_autogen2 style=width: 6px. In fact, I started seeing this after I upgraded a previous install - and based on this behavior, I did a complete re-install, but am still getting it. Does anyone know whether or not this has been fixed and pushed back to repository so we can pull the fix? On Fri, Mar 1, 2013 at 3:59 PM, Kelvin Chan kelvin.c...@seqmatic.com wrote: Hello, I am having a slight issue with the Datatype tab of the edit page. I am using a locally installed version of galaxy-dist obtained from bitbucket. I cannot see anything in the dropdown menu to change the datatype. According to the HTML, the box is only 8px wide. div class=select2-container id=s2id_autogen2 style=width: 8px Is there any way to fix this problem without having to re-install galaxy? Thanks, Kelvin ___ 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: http://lists.bx.psu.edu/ -- Peter Waltman, Ph.D. pwalt...@ucsc.edu 617.347.1876 ___ 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: http://lists.bx.psu.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: http://lists.bx.psu.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: http://lists.bx.psu.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: http://lists.bx.psu.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: http://lists.bx.psu.edu/ -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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
Re: [galaxy-dev] Datatype dropdown only 8px wide
The fix for this issue is in revision 0ea9f5196fde, see: https://bitbucket.org/galaxy/galaxy-central/commits/0ea9f5196fde This is not yet available in galaxy-dist, but will be in the near future. -Dannon On Wed, Mar 13, 2013 at 9:05 PM, Nikhil Joshi najo...@ucdavis.edu wrote: P.S. I am not a galaxy developer :) On Wed, Mar 13, 2013 at 6:04 PM, Nikhil Joshi najo...@ucdavis.edu wrote: Can someone point me to where this fix is... I can't find it anywhere and I am running into this problem as well. - Nik. On Mon, Mar 4, 2013 at 9:54 AM, Kelvin Chan kelvin.c...@seqmatic.com wrote: Nevermind, I noticed that the wiki page on Install galaxy was recently updated to show how to do this. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Kelvin Chan Sent: Monday, March 04, 2013 9:50 AM To: 'Nate Coraor'; 'Björn Grüning' Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Datatype dropdown only 8px wide Hi Nate, I have checked and I am indeed in the Default branch. Is there an easy way to switch over to the stable branch via command line? -Kelvin -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: Monday, March 04, 2013 8:52 AM To: Björn Grüning Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Datatype dropdown only 8px wide All, Could you check whether you are running the default or stable branch of galaxy-dist? You can find out with the `hg branch` command. I believe this problem should only exist if you're running the default (development) branch, which is not recommended. Thanks, --nate On Mar 4, 2013, at 1:17 AM, Björn Grüning wrote: Hi Peter, i think it was fixed in 0ea9f51. You need to adopt static/style/base.less. Cheers, Bjoern I'm seeing something similar with a local galaxy-dist install that was also installed from bitbucket about 1.5-2 weeks ago, however, in my case, the width is set to 6px, e.g. div class=select2-container id=s2id_autogen2 style=width: 6px. In fact, I started seeing this after I upgraded a previous install - and based on this behavior, I did a complete re-install, but am still getting it. Does anyone know whether or not this has been fixed and pushed back to repository so we can pull the fix? On Fri, Mar 1, 2013 at 3:59 PM, Kelvin Chan kelvin.c...@seqmatic.com wrote: Hello, I am having a slight issue with the Datatype tab of the edit page. I am using a locally installed version of galaxy-dist obtained from bitbucket. I cannot see anything in the dropdown menu to change the datatype. According to the HTML, the box is only 8px wide. div class=select2-container id=s2id_autogen2 style=width: 8px Is there any way to fix this problem without having to re-install galaxy? Thanks, Kelvin ___ 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: http://lists.bx.psu.edu/ -- Peter Waltman, Ph.D. pwalt...@ucsc.edu 617.347.1876 ___ 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: http://lists.bx.psu.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: http://lists.bx.psu.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: http://lists.bx.psu.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: http://lists.bx.psu.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: http://lists.bx.psu.edu/ -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics
[galaxy-dev] multiple file output
Hi,
I am trying to right a tool that will generate 2 ouptuts, 1 .txt and .gz.
Before the tools runs I don't know how many fasta files will be in the .gz
file.
I have managed to have the perl script writing files like follow :
$seqio_obj = Bio::SeqIO-new(-file = $seq_library_name, -format = fasta
);
while ($seq_obj = $seqio_obj-next_seq)
{
$seq_ID = $seq_obj - display_id;
$seq = $seq_obj - seq;
#print $seq_ID.\n;
#print $MID_id_ref{$seq_ID}.\n;
if (defined($combination{$seq_ID}))
{
open(OUT,/my/own/path/on/my/server/which
/is/not/good/.$combination{$seq_ID}._library.fasta)||diePb ouverture du
fichier3;
print OUT .$seq_ID.\n.$seq.\n;
#open(OUT,.$output_name2)||diePb ouverture du fichier3;
#print OUT .$seq_ID.\n.$seq.\n;
}
else
{
open(OUT,/my/own/path/on/my/server/which
/is/not/good/unsorted_library.fasta)||diePb ouverture du fichier3;
print OUT .$seq_ID.\n.$seq.\n;
#open(OUT,.$output_name2)||diePb ouverture du fichier3;
#print OUT .$seq_ID.\n.$seq.\n;
$nb_unsorted_seq++;
}
$nb_total_seq++;
}
I then use a command line to zip as follow :
system('cd $work_dir');
system('tar -zcPf '.$output_name2.' /my/own/path/on/my/server/which
/is/not/good/');
If one of you have encounter the same problem or if you can point me to a
tool which is doing some similar stuff.
Thanks,
Philippe
___
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and other Galaxy lists, please use the interface at:
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