Re: [galaxy-dev] firezilla not working

[Nate Coraor]

Hi Atanu and Antara,

This output indicates that your connection has succeeded and you were able
to authenticate, but the switch to passive mode has failed. This most often
occurs due to firewalls which inspect packets sent to the FTP control port
(21) in order to read the PASV command to configure access through the
firewall dynamically. I've posted some information about this process on
our Biostars site here:

  https://biostar.usegalaxy.org/p/24920/#24930

If switching to implicit FTPS does not solve the problem for you, please
check with the network or security administrators at your site to see if
outbound ports in the range 3-31000 are blocked, and whether they can
be allowed, at least to the Galaxy FTP servers.

--nate



On Tue, Mar 20, 2018 at 6:38 AM, Atanu Pan  wrote:

> Hi,
>
> This is an intermittent problem, sometime it is connected and sometime not.
> The error is attached in the file, please help.
>
> Regards,
> Atanu Pan
> --
> *From: *"Antara Biswas" 
> *To: *galaxy-dev@lists.galaxyproject.org
> *Cc: *"Atanu Pan" 
> *Sent: *Tuesday, March 20, 2018 12:19:57 PM
> *Subject: *firezilla not working
>
> Dear galaxy team,
>
> I am having trouble since a week uploading data into filezilla from local
> computer. Error message says- connection refused by server. Please help.
> My login id is a...@nibmg.ac.in
>
> Thanks
> Antara Biswas
> Research Fellow
> National Institute of Biomedical Genomics
> India
>
>
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[galaxy-dev] FileZilla not working

[Antara Biswas]

Dear galaxy team, 

I am having trouble since a week uploading data from local computer into 
FileZilla using FTP for transfer to galaxy server. Error message says- 
connection refused by server. Please help. 
My login id is a...@nibmg.ac.in 

Thanks 
Antara Biswas 
Research Fellow 
National Institute of Biomedical Genomics 
India 
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Re: [galaxy-dev] Problems installing Galaxy 18.01

[Peter van Heusden]

Thanks to Marius and others, I now have a working Galaxy server, including
CVMFS support, as documented in the complete blog post:
http://pvh.wp.sanbi.ac.za/2018/03/18/galaxy-18-01-install/

The problem I was encountering with installations was related to incorrect
environment configuration, which led to the `hg` binary not being found in
the PATH and thus the install failing. Another fault led to this failure
being a silent failure.

I've linked to the working configuration in the blog, but here is a direct
link:

https://gist.github.com/pvanheus/589f84507a26ffa49e3bdf3bd938f25c

It is rather too unwieldy to paste here.

Note that while the says [program:web], there is only one section in the
supervisord configuration. The server is running in a uWSGI + Mules
configuration.

Thanks!
Peter



On Mon, 19 Mar 2018 at 11:17 Peter van Heusden  wrote:

> First to answer your questions:
>
> I'm on release_18.01 branch,
> commit c58ca749c26bbb3c4ca8750f2c37fd1bb6bd7999.
>
> Thanks for the note about nginx-extras, I've installed that and it fixes
> the upload
> directives problem.
>
> Then on to the main problem. I used "Get Data" as the default location
> because I'm really just testing the install. The install goes from "New"
> status to "Error" status pretty much immediately:
>
> [image: image.png]
>
> This is not a bowtie2-specific problem, I get the same behaviour when
> trying to install fastqc.
>
> Thanks for your reply,
> Peter
> P.S. running already-installed tools works
>
> On Mon, 19 Mar 2018 at 09:44 Marius van den Beek 
> wrote:
>
>> Hi Peter,
>>
>> does the tool show up in the tool panel (Looks like you've installed it
>> into "Get Data")?
>> What commit are you on ? There were some last minute bugfixes to the
>> release_18.01
>> prior to the release, so if the checkout is a few days old an upgrade
>> (and an uninstall/install cycle) might help.
>>
>> Also you mentioned the lack of the upload_store in nginx in nginx, you
>> need to install nginx-extras, not nginx.
>>
>> Hope that helps,
>> Marius
>>
>> On 18 March 2018 at 21:17, Peter van Heusden  wrote:
>>
>>> Hi there
>>>
>>> My newly installed Galaxy 18.01 server seems to be unable to install
>>> bowtie (the devteam version). I'm documenting my installation progress at:
>>>
>>> http://pvh.wp.sanbi.ac.za/2018/03/18/galaxy-18-01-install/
>>>
>>> As noted in the last paragraph:
>>>
>>> "My next test was to try and install the bowtie2 tool from the toolshed.
>>> This failed, with the tool status going from New to Error with not much
>>> interesting left in the logs."
>>>
>>> The log during the time when I'm trying to install bowtie2 is:
>>>
>>>
>>>1. [pid: 8856|app: 0|req: 35/48] 10.8.0.2 () {48 vars in 1108 bytes}
>>>[Sun Mar 18 19:14:55 2018] GET
>>>/admin_toolshed/manage_repository?id=f597429621d6eb2b=install 
>>> =>
>>>generated 650 bytes in 26 msecs (HTTP/1.1 302) 3headers in 269 bytes
>>>(1 switches on core 1)
>>>2. 10.8.0.2 - - [18/Mar/2018:19:14:57 +] "GET
>>>/admin_toolshed/manage_repository?id=f597429621d6eb2b=install
>>>HTTP/1.1" 302 - "
>>>
>>> https://galaxy.sanbi.ac.za/admin_toolshed/manage_repository?id=f597429621d6eb2b;
>>>"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like
>>>Gecko) Chrome/65.0.3325.146 Safari/537.36"
>>>3. [pid: 8856|app: 0|req: 37/49] 10.8.0.2 () {48 vars in 1108 bytes}
>>>[Sun Mar 18 19:14:57 2018] GET
>>>/admin_toolshed/manage_repository?id=f597429621d6eb2b=install 
>>> =>
>>>generated 650 bytes in 24 msecs (HTTP/1.1 302) 3headers in 269 bytes
>>>(1 switches on core 0)
>>>4. galaxy.tools.deps DEBUG 2018-03-18 19:14:59,375 [p:8856,w:2,m:0] [
>>>uWSGIWorker2Core2] Dependency bowtie2 not found.
>>>5. galaxy.tools.deps DEBUG 2018-03-18 19:14:59,376 [p:8856,w:2,m:0] [
>>>uWSGIWorker2Core2] Dependency samtools not found.
>>>6. galaxy.tools.deps DEBUG 2018-03-18 19:15:00,028 [p:8856,w:2,m:0] [
>>>uWSGIWorker2Core3] Dependency bowtie2 not found.
>>>7. galaxy.tools.deps DEBUG 2018-03-18 19:15:00,028 [p:8856,w:2,m:0] [
>>>uWSGIWorker2Core3] Dependency samtools not found.
>>>8. 10.8.0.2 - - [18/Mar/2018:19:14:55 +] "GET
>>>
>>> /admin_toolshed/prepare_for_install?changeset_revisions=dc1639b66f12_ids=126c0918b5459666_shed_url=https%3A%2F%
>>>2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 200 - "
>>>
>>> https://galaxy.sanbi.ac.za/admin_toolshed/manage_repository?id=f597429621d6eb2b;
>>>"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like
>>>Gecko) Chrome/65.0.3325.146 Safari/537.36"
>>>9. [pid: 8856|app: 0|req: 38/50] 10.8.0.2 () {48 vars in 1274 bytes}
>>>[Sun Mar 18 19:14:55 2018] GET
>>>
>>> /admin_toolshed/prepare_for_install?changeset_revisions=dc1639b66f12_ids=126c0918b5459666_shed_url=https%3A%2F%
>>>2Ftoolshed.g2.bx.psu.edu%2F => generated 19062 bytes in 7001 msecs (
>>>HTTP/1.1 200) 2 headers in