Re: [galaxy-dev] sending data

[Jennifer Hillman-Jackson]

Hello,

Galaxy accepts data using *passive FTP*. This client will send data that
way but also in various secure modes. Please try using passive mode.

Thanks!

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Tue, Aug 16, 2016 at 7:27 AM, Labdros drosophila  wrote:

> In the last two days I'm dificuldaddes techniques to send my data by BAREFTP 
> , I wanted to know if there is anything wrong by port 21 or the server?
>
> Thank you for your attention and sorry for any inconvenience.
>
>
>
> ___
> 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/
>
___
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/

[galaxy-dev] Docker ToolShed Imports Issue

[Yip, Miu ki]

Hi all,

I’m trying to import shed tools into Galaxy for Docker. When I build the 
container, I get this error message:

TASK [galaxy_tools : Install Tool Shed tools] **
 [WARNING]: The loop variable 'item' is already in use. You should set the
`loop_var` value in the `loop_control` option for the task to something else to
avoid variable collisions and unexpected behavior.
failed: [localhost] (item={u'owner': u'vlefort', u'tool_shed_url': 
u'https://toolshed.g2.bx.psu.edu', 
u'tool_panel_section_label': u'Import Files', u'name': u'phyml'}) => 
{"changed": false, "cmd": ["/tmp/venv/bin/python", 
"install_tool_shed_tools.py", "-y", "name: phyml\nowner: 
vlefort\ntool_panel_section_label: Import Files\ntool_shed_url: 
https://toolshed.g2.bx.psu.edu\n;, "-a", "admin", "-g", "localhost:8080"], 
"delta": "0:00:00.781449", "end": "2016-08-17 23:48:07.389199", "failed": true, 
"failed_when_result": true, "item": {"name": "phyml", "owner": "vlefort", 
"tool_panel_section_label": "Import Files", "tool_shed_url": 
"https://toolshed.g2.bx.psu.edu"}, "rc": 0, "start": "2016-08-17 
23:48:06.607750", "stderr": "(1/1) Installing tool phyml from vlefort to 
section \"Import Files\" at revision f6dadc1de75f (TRT: 0:00:00.308611)\r\n\t* 
Error installing a tool (after phyml)! Name: 0:00:00.247213,owner: vlefort, 
revision: f6dadc1de75f, error: {\"err_msg\": \"Missing required parameter 
'shed_tool_conf'.\", \"err_code\": 47}\r\nInstalled tools (0): 
[]\r\nSkipped tools (0): []\r\nErrored tools (1): [('phyml', 
u'f6dadc1de75f')]\r\nAll tools listed in 'None' have been processed.\r\nTotal 
run time: 0:00:00.556216", "stdout": "", "stdout_lines": [], "warnings": []}
…ignoring

Is this a conf file issue?

Best,
Miuki
___
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/

[galaxy-dev] sending data

[Labdros drosophila]

In the last two days I'm dificuldaddes techniques to send my data by
BAREFTP , I wanted to know if there is anything wrong by port 21 or
the server?

Thank you for your attention and sorry for any inconvenience.
___
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/

[galaxy-dev] Issue when using xsendfile with galaxy release_16.07

[SAPET, Frederic]

Hello

I'm trying the latest Galaxy (git status gives me : # On branch release_16.07)

I've set the xsend option in galaxy.ini (in order to run Galaxy behind a web 
server proxy, and apply all methods described here : 
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy)
apache_xsendfile = True

HTML, gff3,tabular files are just fine but the preview of some other files 
(txt, csv)  is broken on the interface.

When I want to preview a txt file :
Not Found
The requested URL /datasets/fd1df6a9052810d5/display/ was not found on this 
server.

And apache says :
[Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12] (13)Permission 
denied: xsendfile: cannot open file: 
/softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer: http:

But it looks like this is not really a problem related to access.
Indeed, from the same file, I switch it from txt to tabular (edit attributes), 
the preview works.

Are you able to reproduce the behavior ?
The same problem occurs on release_16.01.
It's fine with  the release v15.05 which is my production server right now.

Fred

___
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/

[galaxy-dev] Workflow ID, Galaxy Instance URL, API Key in Galaxy Tool Config

[Katherine Beaulieu]

Hi everyone,
We are trying to obtain the three things in the tile of this post to enable
a tool to use the bioblend api and get the .ga file so that any user can go
back into our system, get the workflow associated with the end file, get
the input parameters which are tags associated with the end file, and rerun
that workflow if necessary. So simply put I am asking if there is a way to
access a galaxy instance through the bioblend api from within a tool's
config xml file.

I have asked about getting the .ga file beforehand but still have not
solved this problem so if anyone has any experience with this please let me
know.
Cheers,
Katherine
___
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/