Clone Galaxy from repository: mercurial from behind proxy?

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Clone Galaxy from repository: mercurial from behind proxy?

Sebastian Schaaf
Hi all,

I'm currently trying to set up a galaxy-dist instance on a SLES server
within an 'encapsulated' network (hospital environment; here all
sensitive data is stored and handled). Within this network, clients are
only capable of accessing the internet via HTTP/HTTPS and FTP, using a
proxy - adress and port (8080) are the same for all three protocols.

Mercurial (which I had to set up in advance) is accessible and more or
less in default configuration (more on that down below).

What I get after executing the command 'hg clone
https://bitbucket.org/galaxy/galaxy-dist#stable'
is
"abort: error: _ssl.c:491: error:140700FC:SSL
routines:SSL23_GET_SERVER_HELLO:unknown protocol"

Google search indicates something more general, so outside the exclusive
scope of Galaxy. On top, no connection to Galaxy was listed, also not in
this mailing list's archive.

Following some hints I just tried to set the proxy via a '.hgrc' file in
the galaxy user home like this:
---
[http_proxy]
host = url:port

[https_proxy]
host = url:port
---
(re-login after that) and also set the system variables '$http_proxy'
and '$https_proxy'. Another approach described was to call
'hg --config http_proxy.host=url:port clone
https://bitbucket.org/galaxy/galaxy-dist#stable'

Nothing worked out.

Does anyone experienced similar behaviour or has got some ideas how to
solve this?

Thanks in advance,

Sebastian


--
Sebastian Schaaf, M.Sc. Bioinformatics
University of Munich

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Re: Clone Galaxy from repository: mercurial from behind proxy?

saketkc
Hi Sebastian,


I work behind a proxy too(In my case I have to supply a username and password too )

I have the following thins setup in my ~/.bashrc:

export http_proxy= http://username:password@proxy-url:proxy-port/

then source it:
$ source ~/.bashrc

or maybe relogin .

and the .hgrc settings that you have specified usually work for me  smoothly.

Here are few links that I remember using . I am no longer behind a proxy , so would not be able to verify this now, Though I remember pushing and pulling from behind proxy using the above settings

1. http://www.jameswampler.com/2010/06/10/configure-mercurial-hg-to-use-a-proxy-server/
2.http://stackoverflow.com/questions/8991608/configuration-for-using-mercurial-with-bitbucket-from-behind-a-certificate-rewri



On 18 June 2013 19:48, Sebastian Schaaf <[hidden email]> wrote:
Hi all,

I'm currently trying to set up a galaxy-dist instance on a SLES server within an 'encapsulated' network (hospital environment; here all sensitive data is stored and handled). Within this network, clients are only capable of accessing the internet via HTTP/HTTPS and FTP, using a proxy - adress and port (8080) are the same for all three protocols.

Mercurial (which I had to set up in advance) is accessible and more or less in default configuration (more on that down below).

What I get after executing the command 'hg clone https://bitbucket.org/galaxy/galaxy-dist#stable'
is
"abort: error: _ssl.c:491: error:140700FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown protocol"

Google search indicates something more general, so outside the exclusive scope of Galaxy. On top, no connection to Galaxy was listed, also not in this mailing list's archive.

Following some hints I just tried to set the proxy via a '.hgrc' file in the galaxy user home like this:
---
[http_proxy]
host = url:port

[https_proxy]
host = url:port
---
(re-login after that) and also set the system variables '$http_proxy' and '$https_proxy'. Another approach described was to call
'hg --config http_proxy.host=url:port clone https://bitbucket.org/galaxy/galaxy-dist#stable'

Nothing worked out.

Does anyone experienced similar behaviour or has got some ideas how to solve this?

Thanks in advance,

Sebastian


--
Sebastian Schaaf, M.Sc. Bioinformatics
University of Munich

___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Clone Galaxy from repository: mercurial from behind proxy?

saketkc
You might want to ssh out and check if that is allowed. If you can ssh out,
you should be able to clone from bitbucket ssh too [ Though you might not be able to push, depending on whether or not you own the repository]


On 18 June 2013 19:59, Saket Choudhary <[hidden email]> wrote:
Hi Sebastian,


I work behind a proxy too(In my case I have to supply a username and password too )

I have the following thins setup in my ~/.bashrc:

export http_proxy= http://username:password@proxy-url:proxy-port/

then source it:
$ source ~/.bashrc

or maybe relogin .

and the .hgrc settings that you have specified usually work for me  smoothly.

Here are few links that I remember using . I am no longer behind a proxy , so would not be able to verify this now, Though I remember pushing and pulling from behind proxy using the above settings

1. http://www.jameswampler.com/2010/06/10/configure-mercurial-hg-to-use-a-proxy-server/
2.http://stackoverflow.com/questions/8991608/configuration-for-using-mercurial-with-bitbucket-from-behind-a-certificate-rewri



On 18 June 2013 19:48, Sebastian Schaaf <[hidden email]> wrote:
Hi all,

I'm currently trying to set up a galaxy-dist instance on a SLES server within an 'encapsulated' network (hospital environment; here all sensitive data is stored and handled). Within this network, clients are only capable of accessing the internet via HTTP/HTTPS and FTP, using a proxy - adress and port (8080) are the same for all three protocols.

Mercurial (which I had to set up in advance) is accessible and more or less in default configuration (more on that down below).

What I get after executing the command 'hg clone https://bitbucket.org/galaxy/galaxy-dist#stable'
is
"abort: error: _ssl.c:491: error:140700FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown protocol"

Google search indicates something more general, so outside the exclusive scope of Galaxy. On top, no connection to Galaxy was listed, also not in this mailing list's archive.

Following some hints I just tried to set the proxy via a '.hgrc' file in the galaxy user home like this:
---
[http_proxy]
host = url:port

[https_proxy]
host = url:port
---
(re-login after that) and also set the system variables '$http_proxy' and '$https_proxy'. Another approach described was to call
'hg --config http_proxy.host=url:port clone https://bitbucket.org/galaxy/galaxy-dist#stable'

Nothing worked out.

Does anyone experienced similar behaviour or has got some ideas how to solve this?

Thanks in advance,

Sebastian


--
Sebastian Schaaf, M.Sc. Bioinformatics
University of Munich

___________________________________________________________
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/

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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Clone Galaxy from repository: mercurial from behind proxy?

Sebastian Schaaf
Hi Saket,

First of all thanks a lot for your really quick reply. To sum it up: you
were right.

After ensuring the SSH out (works) your comments led me to the idea to
test the 'hg clone' command with a user account, which is neither root
nor galaxy. These two are local users, while my personal account is from
a LDAP server. Your hint to include username and password into the
http:proxy variable was the key: only LDAP users seem to be allowed to
pass the proxy or better: if those users are already logged in, username
and password are already implicitly deposited.

Thus, the cloning process as the LDAP user (did not want to store the
foreign username/password explicitly in the galaxy user files) worked,
although I get this message:
"*** failed to import extension hgext.imerge: no module named imerge"
(once at the process' beginning and once at the end)

Anyway, this seems to be more a warning than an error. I found
possibility to silence it, but would like to understand what the missing
may cause.

Any clue, anyone?



Saket Choudhary schrieb:

> You might want to ssh out and check if that is allowed. If you can ssh
> out,
> you should be able to clone from bitbucket ssh too [ Though you might
> not be able to push, depending on whether or not you own the repository]
>
>
> On 18 June 2013 19:59, Saket Choudhary <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Sebastian,
>
>
>     I work behind a proxy too(In my case I have to supply a username
>     and password too )
>
>     I have the following thins setup in my ~/.bashrc:
>
>     export http_proxy= <a href="http://username:password@proxy-url:proxy-port/">http://username:password@proxy-url:proxy-port/
>
>     then source it:
>     $ source ~/.bashrc
>
>     or maybe relogin .
>
>     and the .hgrc settings that you have specified usually work for
>     me  smoothly.
>
>     Here are few links that I remember using . I am no longer behind a
>     proxy , so would not be able to verify this now, Though I remember
>     pushing and pulling from behind proxy using the above settings
>
>     1.
>     http://www.jameswampler.com/2010/06/10/configure-mercurial-hg-to-use-a-proxy-server/
>     2.http://stackoverflow.com/questions/8991608/configuration-for-using-mercurial-with-bitbucket-from-behind-a-certificate-rewri
>
>
>
>     On 18 June 2013 19:48, Sebastian Schaaf
>     <[hidden email]
>     <mailto:[hidden email]>> wrote:
>
>         Hi all,
>
>         I'm currently trying to set up a galaxy-dist instance on a
>         SLES server within an 'encapsulated' network (hospital
>         environment; here all sensitive data is stored and handled).
>         Within this network, clients are only capable of accessing the
>         internet via HTTP/HTTPS and FTP, using a proxy - adress and
>         port (8080) are the same for all three protocols.
>
>         Mercurial (which I had to set up in advance) is accessible and
>         more or less in default configuration (more on that down below).
>
>         What I get after executing the command 'hg clone
>         https://bitbucket.org/galaxy/galaxy-dist#stable'
>         is
>         "abort: error: _ssl.c:491: error:140700FC:SSL
>         routines:SSL23_GET_SERVER_HELLO:unknown protocol"
>
>         Google search indicates something more general, so outside the
>         exclusive scope of Galaxy. On top, no connection to Galaxy was
>         listed, also not in this mailing list's archive.
>
>         Following some hints I just tried to set the proxy via a
>         '.hgrc' file in the galaxy user home like this:
>         ---
>         [http_proxy]
>         host = url:port
>
>         [https_proxy]
>         host = url:port
>         ---
>         (re-login after that) and also set the system variables
>         '$http_proxy' and '$https_proxy'. Another approach described
>         was to call
>         'hg --config http_proxy.host=url:port clone
>         https://bitbucket.org/galaxy/galaxy-dist#stable'
>
>         Nothing worked out.
>
>         Does anyone experienced similar behaviour or has got some
>         ideas how to solve this?
>
>         Thanks in advance,
>
>         Sebastian
>
>
>         --
>         Sebastian Schaaf, M.Sc. Bioinformatics
>         University of Munich
>
>         ___________________________________________________________
>         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/
>
>         To search Galaxy mailing lists use the unified search at:
>         http://galaxyproject.org/search/mailinglists/
>
>
>


--
Sebastian Schaaf, M.Sc. Bioinformatics
Faculty Coordinator NGS Infrastructure
Chair of Biometry and Bioinformatics
Department of Medical Informatics,
  Biometry and Epidemiology (IBE)
University of Munich
Marchioninistr. 15, K U1 (postal)
Marchioninistr. 17, U 006 (office)
D-81377 Munich (Germany)
Tel: +49 89 2180-78178

___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
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Re: Clone Galaxy from repository: mercurial from behind proxy?

Dannon Baker-2
On Tue, Jun 18, 2013 at 10:54 AM, Sebastian Schaaf <[hidden email]> wrote:
Thus, the cloning process as the LDAP user (did not want to store the foreign username/password explicitly in the galaxy user files) worked, although I get this message:
"*** failed to import extension hgext.imerge: no module named imerge"
(once at the process' beginning and once at the end)

Anyway, this seems to be more a warning than an error. I found possibility to silence it, but would like to understand what the missing may cause.

Any clue, anyone?

Imerge is an old extension that used to ship with mercurial.  Check your .hgrc file for the [extensions] section and make sure there's no line for imerge.  If there is, remove it -- recent versions of mercurial don't use this anymore.
 

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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Clone Galaxy from repository: mercurial from behind proxy?

Sebastian Schaaf
Thanks for the hint - that may be due to the fact that mercurial as
package only comes via a repository dating back to SLES 11 SP1 - there
seems to be no newer one. I just looked up the version: instead of
current v2.6.2 it's v1.0.2 (!)
On the other hand I'm glad that this reads like it does not affect
galaxy. btw: just started the server up, no complains yet.


Dannon Baker schrieb:

> On Tue, Jun 18, 2013 at 10:54 AM, Sebastian Schaaf
> <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Thus, the cloning process as the LDAP user (did not want to store
>     the foreign username/password explicitly in the galaxy user files)
>     worked, although I get this message:
>     "*** failed to import extension hgext.imerge: no module named imerge"
>     (once at the process' beginning and once at the end)
>
>     Anyway, this seems to be more a warning than an error. I found
>     possibility to silence it, but would like to understand what the
>     missing may cause.
>
>     Any clue, anyone?
>
>
> Imerge is an old extension that used to ship with mercurial.  Check
> your .hgrc file for the [extensions] section and make sure there's no
> line for imerge.  If there is, remove it -- recent versions of
> mercurial don't use this anymore.


--
Sebastian Schaaf, M.Sc. Bioinformatics
Faculty Coordinator NGS Infrastructure
Chair of Biometry and Bioinformatics
Department of Medical Informatics,
  Biometry and Epidemiology (IBE)
University of Munich
Marchioninistr. 15, K U1 (postal)
Marchioninistr. 17, U 006 (office)
D-81377 Munich (Germany)
Tel: +49 89 2180-78178

___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/