[galaxy-dev] tool for RepeatMasker?

[Smithies, Russell]

Has anyone created a tool for running RepeatMasker http://www.repeatmasker.org/ 
within Galaxy?
It's something we'd like to do so we can create workflows where the fasta is 
masked before being searched with blast.

Thanx,

Russell Smithies
New Zealand

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Re: [galaxy-dev] tool for RepeatMasker?

[Smithies, Russell]

Hi Björn,
I'd be keen to test it before release if that's OK.
I'm surprised there's not one already? I would have thought it was a key tool 
in most bioinformaticians toolbox.


Thanx,


Russell Smithies
Infrastructure Team
T 03 489 9085
M 0274 734 600
E russell.smith...@agresearch.co.nz

Invermay Agricultural Centre
Puddle Alley, Private Bag 50034, Mosgiel 9053, New Zealand
T  +64 3 489 3809  F  +64 3 489 3739  www.agresearch.co.nz



> -Original Message-
> From: Björn Grüning [mailto:bjoern.gruen...@pharmazie.uni-freiburg.de]
> Sent: Monday, 28 November 2011 12:12 p.m.
> To: Smithies, Russell
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> Subject: Re: [galaxy-dev] tool for RepeatMasker?
> 
> Hi Russell,
> 
> i have a working wrapper. I will upload it to the toolshed soon, but if you 
> like
> to test it before, that would be nice.
> 
> kind regards,
> Bjoern
> 
> Am Montag, den 28.11.2011, 11:57 +1300 schrieb Smithies, Russell:
> > Has anyone created a tool for running RepeatMasker
> > http://www.repeatmasker.org/ within Galaxy?
> >
> > It’s something we’d like to do so we can create workflows where the
> > fasta is masked before being searched with blast.
> >
> >
> >
> > Thanx,
> >
> >
> >
> > Russell Smithies
> >
> > New Zealand
> >
> >
> >
> >
> >
> >
> __
> 
> >
> > Attention: The information contained in this message and/or
> > attachments from AgResearch Limited is intended only for the persons
> > or entities to which it is addressed and may contain confidential
> > and/or privileged material. Any review, retransmission, dissemination
> > or other use of, or taking of any action in reliance upon, this
> > information by persons or entities other than the intended recipients
> > is prohibited by AgResearch Limited. If you have received this message
> > in error, please notify the sender immediately.
> >
> >
> >
> __
> 
> >
> >
> >
> >
> __
> _
> > Please keep all replies on the list by using "reply all"
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[galaxy-dev] proxy settings?

[Smithies, Russell]

I'm new to Galaxy so I'm not sure if this a Galaxy or linux/apache question .

When I try to "Get Data" from UCSC or any other external site, I get a 407 
error from our proxy as I need to authenticate.
Is the request going out as the 'galaxy' user or 'apache' or the user that's 
logged in?
I already have http_proxy and ftp_proxy configured in /etc/profile (we're 
running Centos 6) but I assume there a correct place to configure this for 
Galaxy?

The error message I'm seeing is:
An error occurred running this job: The remote data source application may be 
off line, please try again later. Error: ('http error', 407, 'Proxy Access 
Denied', )

Any ideas?

Thanx,

Russell Smithies


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Re: [galaxy-dev] proxy settings?

[Smithies, Russell]

Found the cure - just required adding urllib2.ProxyHandler in the data_source 
tools.
Why doesn't Galaxy pick up the system http_proxy variables?

--Russell Smithies


From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Smithies, Russell
Sent: Wednesday, 30 November 2011 9:09 a.m.
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] proxy settings?

I'm new to Galaxy so I'm not sure if this a Galaxy or linux/apache question .

When I try to "Get Data" from UCSC or any other external site, I get a 407 
error from our proxy as I need to authenticate.
Is the request going out as the 'galaxy' user or 'apache' or the user that's 
logged in?
I already have http_proxy and ftp_proxy configured in /etc/profile (we're 
running Centos 6) but I assume there a correct place to configure this for 
Galaxy?

The error message I'm seeing is:
An error occurred running this job: The remote data source application may be 
off line, please try again later. Error: ('http error', 407, 'Proxy Access 
Denied', )

Any ideas?

Thanx,

Russell Smithies






Attention: The information contained in this message and/or attachments from 
AgResearch Limited is intended only for the persons or entities to which it is 
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Re: [galaxy-dev] proxy settings?

[Smithies, Russell]

Hi Nate,
My "solution" was a bit of a hack and there may be better ways of doing it (I 
haven't read all the docs yet - just started with Galaxy last week)
Python is not my strong suit and there may be more elegant ways, but here's how 
I usually connect thru our proxy:

--
proxy_info = {
'user' : 'DOMAIN\\username',
'pass' : 'thisismypassword',
'host' : "proxy.yoyodyne.com",
'port' : 8080
}
# build a new opener that uses a proxy requiring authorization
proxy_support = urllib2.ProxyHandler({"http" : 
"http://%(user)s:%(pass)s@%(host)s:%(port)d" % proxy_info})
opener = urllib2.build_opener(proxy_support, urllib2.HTTPHandler)

# install it
urllib2.install_opener(opener)

#then open the page with urllib2
page = urllib2.urlopen( cur_URL )
--

I was in a hurry so tweaked data_source.py,  fetch.py,  
genomespace_file_browser.py,  ucsc_proxy.py, and  upload.py but it would make 
more sense to read the proxy_info from universe_wsgi.ini 
If you can point me at an example of a tool that reads from the config, I'll 
try and put it together.
The best solution would be for Python to pick up the local $http_proxy env 
settings but I've never managed to get that working!

--Russell




> -Original Message-
> From: Nate Coraor [mailto:n...@bx.psu.edu]
> Sent: Friday, 2 December 2011 7:03 a.m.
> To: Smithies, Russell
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] proxy settings?
> 
> On Nov 29, 2011, at 9:35 PM, Smithies, Russell wrote:
> 
> > Found the cure - just required adding urllib2.ProxyHandler in the
> data_source tools.
> > Why doesn't Galaxy pick up the system http_proxy variables?
> 
> Hi Russell,
> 
> Thanks for tracking down the problem.  Could you send a patch for this?
> 
> --nate
> 
> >
> > --Russell Smithies
> >
> >
> > From: galaxy-dev-boun...@lists.bx.psu.edu
> > [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Smithies,
> > Russell
> > Sent: Wednesday, 30 November 2011 9:09 a.m.
> > To: galaxy-dev@lists.bx.psu.edu
> > Subject: [galaxy-dev] proxy settings?
> >
> > I'm new to Galaxy so I'm not sure if this a Galaxy or linux/apache question 
> > .
> >
> > When I try to "Get Data" from UCSC or any other external site, I get a 407
> error from our proxy as I need to authenticate.
> > Is the request going out as the 'galaxy' user or 'apache' or the user that's
> logged in?
> > I already have http_proxy and ftp_proxy configured in /etc/profile (we're
> running Centos 6) but I assume there a correct place to configure this for
> Galaxy?
> >
> > The error message I'm seeing is:
> > An error occurred running this job: The remote data source application
> > may be off line, please try again later. Error: ('http error', 407,
> > 'Proxy Access Denied', )
> >
> > Any ideas?
> >
> > Thanx,
> >
> > Russell Smithies
> >
> >
> >
> > Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities to which
> it is addressed and may contain confidential and/or privileged material. Any
> review, retransmission, dissemination or other use of, or taking of any action
> in reliance upon, this information by persons or entities other than the
> intended recipients is prohibited by AgResearch Limited. If you have received
> this message in error, please notify the sender immediately.
> >
> >
> >
> >
> __
> _
> > Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] PATH env variable for SGE jobs

[Smithies, Russell]

I had a similar problem where $PATH doesn't appear to be getting read but mine 
was with the EMBOSS packages.
I cheated a bit and just put the full path for the executables in the command:

perl -npi -e 's::/usr/local/bin/:' emboss_*.xml

--Russell

> -Original Message-
> From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-
> boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor
> Sent: Saturday, 3 December 2011 4:42 a.m.
> To: Langhorst, Brad
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] PATH env variable for SGE jobs
> 
> On Dec 1, 2011, at 8:55 PM, Langhorst, Brad wrote:
> 
> > I have the software for our SGE cluster (eg. Bowtie) in
> > /mnt/ngswork/galaxy/sw/bin And I've set the PATH environment in the
> > galaxy user's .bashrc
> >
> > export PATH="/mnt/ngswork/galaxy/sw/bin:$PATH"
> >
> > When I  echo $PATH via qsub as galaxy I do see my path in STDIN.o on
> > the job runner node
> >
> > /mnt/ngswork/galaxy/sw/bin:/tmp/41.1.default.q:/usr/local/bin:/bin:/us
> > r/bin
> > But I always see
> > /bin/sh: bowtie: not found
> >
> > As an error message.
> >
> >
> > How can I get the path set correctly?
> 
> Hi Brad,
> 
> I'd suggest putting it in ~/.sge_request rather than ~/.bashrc.  This will
> ensure that running jobs differently (qsub vs. the DRMAA API) won't affect
> setting $PATH or other environment variables.
> 
> See past discussions on the list for more on .sge_request:
> 
> http://gmod.827538.n3.nabble.com/template/NamlServlet.jtp?macro=searc
> h_page&node=815885&query=sge_request
> 
> --nate
> 
> >
> >
> >
> >
> >
> >
> > Brad
> > --
> > Brad Langhorst
> > New England Biolabs
> > langho...@neb.com
> >
> >
> >
> __
> _
> > Please keep all replies on the list by using "reply all"
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> >
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> 
> 
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[galaxy-dev] possibly weird config requests...

[Smithies, Russell]

This may be a list of weird requests but our Galaxy server runs internally and 
is only accessible to our users so I'd like to make it a bit easier to manage.
I could customize a copy but hopefully some of the "features" I'm after are 
already available. If not, I'm happy to work on them and integrate if others 
think they'll be useful.


* Rather than email address as usernames, we'd rather just use our 
corporate logins (lastname, first initial, eg.mine is smithiesr) Or can I have 
an alias list (like samba)?

* Is there a bulk user creation script? Rather than have everyone 
create their own account, I'd rather do them all at once. It's not that I don't 
trust users but...

* Can I have every user's home dir automagiclly added as a data dir? 
eg. I'd like to have /home/smithiesr available. Would be nice if this was part 
of a bulk useradd script

* Any chance of AD integration? I have no idea if Python plays well 
with Active Directory and/or LDAP.

* Is it possible to add new tools without restarting Galaxy? I know 
tool configs can be reloaded from the admin console but I'd like our users to 
be able to incorporate their existing scripts as tools. Would a local tool-shed 
make this easier?

* We use NTLM for authentication on most of our internal sites - am I 
going to have problems getting Galaxy/Python to authenticate? A few years ago 
we ran into the same requirement with a Java app so ended up hacking together a 
script that passed SSO creds to Internet Exploiter for authentication.

Sorry if some of these sound dumb or are already implemented, I'm still reading 
thru the docs.

Thanx,
Russell Smithies
Infrastructure Team
T 03 489 9085
M 0274 734 600
E russell.smith...@agresearch.co.nz
Invermay Agricultural Centre
Puddle Alley, Private Bag 50034, Mosgiel 9053, New Zealand
T  +64 3 489 3809  F  +64 3 489 3739  www.agresearch.co.nz


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Re: [galaxy-dev] possibly weird config requests...

[Smithies, Russell]

Thanx guys, that should give me heaps to go on with :-)

--Russell

> -Original Message-
> From: Nate Coraor [mailto:n...@bx.psu.edu]
> Sent: Tuesday, 6 December 2011 8:21 a.m.
> To: Ross
> Cc: Smithies, Russell; galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] possibly weird config requests...
> 
> On Dec 4, 2011, at 5:39 PM, Ross wrote:
> 
> > Hi Russell,
> >
> > Just addressing AD/LDAP authentication - authentication is trivially and 
> > best
> (IMHO) left to an external (eg apache) proxy - save yourself a lot of effort -
> it's known to work well.
> > Lock down the paste process so it only talks to your apache and provide
> pass through authentication.
> > Doing that deals with your first and second questions since galaxy will
> create new users as they appear if appropriately configured - although you
> are stuck with user@yourconfigured.domain as the user ids inside Galaxy
> even though the user authenticates with the sAMAccountName in the
> example below so it's the same login for all our AD logins.
> >
> > The recipe has been posted a few times and should be easy to find using a
> search.
> >
> > Something like:
> >
> > 
> >   Options FollowSymLinks
> >   AuthType Basic
> >   AuthBasicProvider ldap
> >   AuthzLDAPAuthoritative Off
> >   AuthName "BHRI LDAP"
> >   Order Allow,Deny
> >   Allow From All
> >   Require valid-user
> >   AuthLDAPBindDN "user@domain"
> >   AuthLDAPBindPassword "passwordforuser@domain"
> >   AuthLDAPURL
> "ldap://172.16.1.245:389/OU=Baker,DC=bhri,DC=internal?sAMAccountName
> ?sub?(objectClass=*)"
> >   RequestHeader set REMOTE_USER
> %{AUTHENTICATE_sAMAccountName}e
> > 
> >
> > works for us on a local AD server
> 
> The documentation for the feature explained by Ross is here:
> 
> http://usegalaxy.org/production
> 
> Responses to other questions follow:
> 
> >
> >
> > On Mon, Dec 5, 2011 at 9:21 AM, Smithies, Russell
>  wrote:
> > This may be a list of weird requests but our Galaxy server runs internally
> and is only accessible to our users so I'd like to make it a bit easier to 
> manage.
> >
> > I could customize a copy but hopefully some of the "features" I'm after are
> already available. If not, I'm happy to work on them and integrate if others
> think they'll be useful.
> >
> >
> >
> > * Rather than email address as usernames, we'd rather just use our
> corporate logins (lastname, first initial, eg.mine is smithiesr) Or can I 
> have an
> alias list (like samba)?
> 
> I know this has been hacked in by another person in their instance, but you
> should also not really need to do this if you use the authentication via proxy
> as explained above.
> 
> > * Is there a bulk user creation script? Rather than have everyone 
> > create
> their own account, I'd rather do them all at once. It's not that I don't trust
> users but...
> 
> Accounts are automatically created when authentication is delegated to the
> upstream proxy server.
> 
> > * Can I have every user's home dir automagiclly added as a data 
> > dir? eg.
> I'd like to have /home/smithiesr available. Would be nice if this was part of 
> a
> bulk useradd script
> 
> Sort of.  You could create a directory of symlinks named as the user's Galaxy
> email address that link to their home directories and then set this directory 
> as
> the value of ftp_upload_dir.  The user would then see the contents of his or
> her home directory on the upload form (but I imagine this would be quite
> slow for large directories).  Instead of their entire directory, I'd suggest 
> using
> a subdirectory or another designated space on the filesystem.
> 
> Importing to a history via the Upload tool may fail if the Galaxy user is 
> unable
> to write to the file and/or directory since this is not what the FTP upload
> functionality was originally designed for.  Documentation is here (not all of 
> it
> is relevant to this non-FTP usage):
> 
> http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP
> 
> > * Any chance of AD integration? I have no idea if Python plays well 
> > with
> Active Directory and/or LDAP.
> >
> > * Is it possible to add new tools without restarting Galaxy? I know 
> > tool
> configs can be reloaded from the admin console but I'd like our users to be
> able to incorporate their existing scripts as tools. Would a local tool-shed
> make this easi

[galaxy-dev] scripts in welcome.html?

[Smithies, Russell]

To stop users forgetting whether they're on our development or production 
servers I'd like to put a simple script in welcome.html to echo the hostname 
(or some other stuff)
I've tried both javascript and php but no luck. Is this supported or should I 
dig further into our Apache config?
Or is there a better way to do it?

Thanx,

Russell Smithies

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Re: [galaxy-dev] scripts in welcome.html?

[Smithies, Russell]

It does of course work, just my scripting skills have faded with lack of use :(

--Russell

From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Smithies, Russell
Sent: Thursday, 14 June 2012 10:37 a.m.
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] scripts in welcome.html?

To stop users forgetting whether they're on our development or production 
servers I'd like to put a simple script in welcome.html to echo the hostname 
(or some other stuff)
I've tried both javascript and php but no luck. Is this supported or should I 
dig further into our Apache config?
Or is there a better way to do it?

Thanx,

Russell Smithies





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[galaxy-dev] re-writing username for login or stripping domain from remote_user?

[Smithies, Russell]

I have a situation I'm sure others have faced but I can't see how to solve it 
without hacking the src and I'd rather not do that just yet as it complicates 
upgrades.

We're using Apache with NTLM and "require valid user" so it's a corporate 
domain and only authorized users are allowed access.
If I set "use_remote_user = True" on universe_wsgi.ini then users are denied as 
Apache is passing the domain and username e.g. REMOTE_USER = DOMAIN\\username
I can't use a rewrite rule to fix it from Apache because then it's an invalid 
username and the user can't log into the web, and if it's passing 
DOMAIN\\username to Galaxy it doesn't match up with the Galaxy username so I 
get a 403 error.
Is there a hidden option to strip the domain from the login or am I going to 
have to start hacking?

Thanx,

Russell Smithies
Infrastructure Technician
Invermay Agricultural Centre
Puddle Alley, Private Bag 50034, Mosgiel 9053, New Zealand
T  +64 3 489 3809  F  +64 3 489 3739  
www.agresearch.co.nz




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[galaxy-dev] NTLM auth not passing http_remote_user?

[Smithies, Russell]

It appears that NTLM isn't passing the HTTP_REMOTE_USER through for us.
Anyone else struck this and found a solution?

Our apache config looks like this:


  AuthName "Galaxy"
  NTLMAuth on
  NTLMAuthHelper "/usr/bin/ntlm_auth --helper-protocol=squid-2.5-ntlmssp"
  NTLMBasicAuthoritative on
  AuthType NTLM
  require valid-user

# Take the $REMOTE_USER environment variable and set it as a header in the 
proxy request.
  RewriteCond %{IS_SUBREQ} ^false$
  RewriteCond %{LA-U:REMOTE_USER} (.+)
  RewriteRule . - [E=RU:%1]
  RequestHeader set REMOTE_USER %{RU}e




thanx,

--Russell

CONTENT_LENGTH
'0'
HTTP_ACCEPT
'*/*'
HTTP_ACCEPT_ENCODING
'gzip, deflate'
HTTP_ACCEPT_LANGUAGE
'en-NZ'
HTTP_AUTHORIZATION
'NTLM bla bla bla'
HTTP_CONNECTION
'Keep-Alive'
HTTP_COOKIE
'__utmc=89232139; 
__utma=89232139.1132753487.1341174446.1342136886.1342560287.3; 
__utmz=89232139.1342560287.3.3.utmcsr=gw.agresearch.co.nz|utmccn=(referral)|utmcmd=referral|utmcct=/Pages/Default.aspx;
 __utmb=89232139.4.10.1342560287; galaxysession=c6ca0dd bla bla bla' bla bla 
bla' bla bla bla' bla bla bla' bla bla bla' bla bla bla' bla bla bla' bla bla 
bla' bla bla bla'
HTTP_HOST
'galaxy-dev.agresearch.co.nz'
HTTP_REMOTE_USER
'(null)'
HTTP_USER_AGENT
'Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 6.1; WOW64; Trident/5.0; SLCC2; 
.NET CLR 2.0.50727; .NET CLR 3.5.30729; .NET CLR 3.0.30729; Media Center PC 
6.0; .NET CLR 1.1.4322; .NET4.0C; .NET4.0E; InfoPath.3)'
HTTP_X_FORWARDED_FOR
'147.158.129.160'
HTTP_X_FORWARDED_HOST
'galaxy-dev.agresearch.co.nz'
HTTP_X_FORWARDED_SERVER
'galaxy.agresearch.co.nz'
ORGINAL_HTTP_HOST
'localhost:8080'
ORGINAL_REMOTE_ADDR
'127.0.0.1'
PATH_INFO
'/'
REMOTE_ADDR
'147.158.129.160'
REQUEST_METHOD
'GET'
SERVER_NAME
'127.0.0.1'
SERVER_PORT
'8080'
SERVER_PROTOCOL
'HTTP/1.1'

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Re: [galaxy-dev] NTLM auth not passing http_remote_user?

[Smithies, Russell]

If I take the rewrite out of the  block then NTLM auth fails as the 
username is re-written and isn't a valid corporate username.
On the plus side, If I just set "RequestHeader set REMOTE_USER smithiesr"  then 
I get logged in as I should.

--Russell


-Original Message-
From: Assaf Gordon [mailto:gor...@cshl.edu] 
Sent: Wednesday, 18 July 2012 9:59 a.m.
To: Smithies, Russell
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] NTLM auth not passing http_remote_user?

Hello Russell,

Smithies, Russell wrote, On 07/17/2012 05:41 PM:
> It appears that NTLM isn't passing the HTTP_REMOTE_USER through for us.
> Anyone else struck this and found a solution?
> 
> Our apache config looks like this:
> 
> 
>   AuthName "Galaxy"
>   NTLMAuth on
>   NTLMAuthHelper "/usr/bin/ntlm_auth --helper-protocol=squid-2.5-ntlmssp"
>   NTLMBasicAuthoritative on
>   AuthType NTLM
>   require valid-user
> 
> # Take the $REMOTE_USER environment variable and set it as a header in 
> the proxy request.
>   RewriteCond %{IS_SUBREQ} ^false$
>   RewriteCond %{LA-U:REMOTE_USER} (.+)
>   RewriteRule . - [E=RU:%1]
>   RequestHeader set REMOTE_USER %{RU}e
> 
> 



> HTTP_REMOTE_USER
> '(null)'


One voodoo solution that worked for me (not with NTLM, but exactly with the 
same '(null)' symptom) is to take the entire "RewriteCond" part outside of the 
 block.
Put it in the global configuration file, after the  part, but before 
the proxy statement.

Also, the exact incantation that worked for me (after many many trials and 
errors) is:
===
RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}] RequestHeader set REMOTE_USER %{RU}e 
===

It's voodoo (to me) because it probably has something to do with deep apache 
internals, relating to execution order of the authentication module vs the 
"mod_rewrite" parts (and the "LA-U" [Look-ahead] thing sure doesn't help to 
make it clearer...).

-gordon


===
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material. Any review, retransmission, dissemination or other use of, or
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Re: [galaxy-dev] NTLM auth not passing http_remote_user?

[Smithies, Russell]

Working now :- )
I blame lack of coffee - I hadn't set "RewriteEngine on" before I re-wrote the 
request header.
It appears it needs to be in the  section or your initial ntlm auth 
wil fail.


  AuthName "Galaxy"
  NTLMAuth on
  NTLMAuthHelper "/usr/bin/ntlm_auth --helper-protocol=squid-2.5-ntlmssp"
  NTLMBasicAuthoritative on
  AuthType NTLM
  require valid-user

# Take the $REMOTE_USER environment variable, trim the realm and set it as 
a header in the proxy request.
  RewriteEngine on
  RewriteCond %{IS_SUBREQ} ^false$
  RewriteCond %{LA-U:REMOTE_USER} .+\\(.+)
  RewriteRule . - [E=RU:%1]
  RequestHeader set REMOTE_USER %{RU}e




--Russell

-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Smithies, Russell
Sent: Wednesday, 18 July 2012 10:52 a.m.
To: Assaf Gordon
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] NTLM auth not passing http_remote_user?

If I take the rewrite out of the  block then NTLM auth fails as the 
username is re-written and isn't a valid corporate username.
On the plus side, If I just set "RequestHeader set REMOTE_USER smithiesr"  then 
I get logged in as I should.

--Russell


-Original Message-
From: Assaf Gordon [mailto:gor...@cshl.edu]
Sent: Wednesday, 18 July 2012 9:59 a.m.
To: Smithies, Russell
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] NTLM auth not passing http_remote_user?

Hello Russell,

Smithies, Russell wrote, On 07/17/2012 05:41 PM:
> It appears that NTLM isn't passing the HTTP_REMOTE_USER through for us.
> Anyone else struck this and found a solution?
> 
> Our apache config looks like this:
> 
> 
>   AuthName "Galaxy"
>   NTLMAuth on
>   NTLMAuthHelper "/usr/bin/ntlm_auth --helper-protocol=squid-2.5-ntlmssp"
>   NTLMBasicAuthoritative on
>   AuthType NTLM
>   require valid-user
> 
> # Take the $REMOTE_USER environment variable and set it as a header in 
> the proxy request.
>   RewriteCond %{IS_SUBREQ} ^false$
>   RewriteCond %{LA-U:REMOTE_USER} (.+)
>   RewriteRule . - [E=RU:%1]
>   RequestHeader set REMOTE_USER %{RU}e
> 
> 



> HTTP_REMOTE_USER
> '(null)'


One voodoo solution that worked for me (not with NTLM, but exactly with the 
same '(null)' symptom) is to take the entire "RewriteCond" part outside of the 
 block.
Put it in the global configuration file, after the  part, but before 
the proxy statement.

Also, the exact incantation that worked for me (after many many trials and 
errors) is:
===
RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}] RequestHeader set REMOTE_USER %{RU}e 
===

It's voodoo (to me) because it probably has something to do with deep apache 
internals, relating to execution order of the authentication module vs the 
"mod_rewrite" parts (and the "LA-U" [Look-ahead] thing sure doesn't help to 
make it clearer...).

-gordon


===
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[galaxy-dev] dns lookup failure and proxy errors from internal toolshed?

[Smithies, Russell]

I'm trying to setup an internal toolshed but am getting DNS and proxy errors:
(I'm using port 8081 instead of 9009)

The proxy server received an invalid response from an upstream server.
The proxy server could not handle the request GET 
/toolshedrepository/browse_valid_repositories.
Reason: DNS lookup failure for: localhost:8081repository

I'm rewriting my URLs like this:

RewriteRule ^/toolshed$ /toolshed/ [R]
RewriteRule ^/toolshed/static/style/(.*) 
/var/lib/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/toolshed/static/scripts/(.*) 
/var/lib/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/toolshed/static/(.*) /var/lib/galaxy/static/$1 [L]
RewriteRule ^/toolshed/favicon.ico /var/lib/galaxy/static/favicon.ico [L]
RewriteRule ^/toolshed/robots.txt /var/lib/galaxy/static/robots.txt [L]
RewriteRule ^/toolshed(.*) http://localhost:8081$1 [P]

I think it might be an Apache problem but no idea hat to try next.

Any ideas?

Thanx,
Russell Smithies
Invermay Agricultural Centre
Puddle Alley, Private Bag 50034, Mosgiel 9053, New Zealand
T  +64 3 489 3809  F  +64 3 489 3739  
www.agresearch.co.nz



===
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Re: [galaxy-dev] dns lookup failure and proxy errors from internal toolshed?

[Smithies, Russell]

I think I see the problem, the URL it's looking for is 
toolshedrepository/browse_valid_repositories<http://galaxy-dev.agresearch.co.nz/toolshedrepository/browse_valid_repositories>
 but it should be 
toolshed/repository/browse_valid_repositories<http://galaxy-dev.agresearch.co.nz/toolshedrepository/browse_valid_repositories>
Was missing a trailing slash in the URL in tool_sheds_conf.xml   :- (

--Russell



From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Smithies, Russell
Sent: Monday, 23 July 2012 3:40 p.m.
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] dns lookup failure and proxy errors from internal 
toolshed?

I'm trying to setup an internal toolshed but am getting DNS and proxy errors:
(I'm using port 8081 instead of 9009)

The proxy server received an invalid response from an upstream server.
The proxy server could not handle the request GET 
/toolshedrepository/browse_valid_repositories<http://galaxy-dev.agresearch.co.nz/toolshedrepository/browse_valid_repositories>.
Reason: DNS lookup failure for: localhost:8081repository

I'm rewriting my URLs like this:

RewriteRule ^/toolshed$ /toolshed/ [R]
RewriteRule ^/toolshed/static/style/(.*) 
/var/lib/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/toolshed/static/scripts/(.*) 
/var/lib/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/toolshed/static/(.*) /var/lib/galaxy/static/$1 [L]
RewriteRule ^/toolshed/favicon.ico /var/lib/galaxy/static/favicon.ico [L]
RewriteRule ^/toolshed/robots.txt /var/lib/galaxy/static/robots.txt [L]
RewriteRule ^/toolshed(.*) http://localhost:8081$1 [P]

I think it might be an Apache problem but no idea hat to try next.

Any ideas?

Thanx,
Russell Smithies
Invermay Agricultural Centre
Puddle Alley, Private Bag 50034, Mosgiel 9053, New Zealand
T  +64 3 489 3809  F  +64 3 489 3739  
www.agresearch.co.nz<http://www.agresearch.co.nz/>








Attention: The information contained in this message and/or attachments from 
AgResearch Limited is intended only for the persons or entities to which it is 
addressed and may contain confidential and/or privileged material. Any review, 
retransmission, dissemination or other use of, or taking of any action in 
reliance upon, this information by persons or entities other than the intended 
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Re: [galaxy-dev] Upload local files

[Smithies, Russell]

Yes, we'd like to do this as well.
Our users data are all on the servers, not on their Windows PCs and requiring 
the admin create shared data libraries is an overhead we'd rather avoid.

Thanx,

Russell Smithies
Infrastructure Technician
T 03 489 9085
M 027 4734 600
E russell.smith...@agresearch.co.nz
Invermay Agricultural Centre
Puddle Alley, Private Bag 50034, Mosgiel 9053, New Zealand
T  +64 3 489 3809  F  +64 3 489 3739  
www.agresearch.co.nz




From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Sascha Kastens
Sent: Tuesday, 31 July 2012 2:09 a.m.
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Upload local files


Hi devs,



when using the upload tool it would be nice to let the user

specify paths to files stored on our internal servers like the admin

can when choosing to add data to a library. Also it would be nice

to be able to link to these files.



Unfortunately I was not able to find the "tool" for uploading

files into a library so it would be nice if you can give me a hint.

With this information I should be able to extend the normal upload

tool.



Thanks in advance!



Cheers,

Sascha Kastens

Project Manager



GATC Biotech AG

Jakob-Stadler-Platz 7

D-78467 Konstanz



Phone: +49 (0) 7531-81604110

Fax: +49 (0) 7531-816081

Email:  s.kast...@gatc-biotech.com



http://www.gatc-biotech.com

http://www.twitter.com/gatcbiotech

http://www.facebook.com/gatcbiotech

http://www.xing.com/companies/gatcbiotechag



GATC Biotech AG
Chairman Supervisory Board: Fritz Pohl
Board of Directors: Peter Pohl, Thomas Pohl, Dr. Marcus Benz
UID: DE 142 315 733 | Registration: Konstanz, HRB 1757 | Registered Office: 
Konstanz





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taken or refrained from in reliance on it, is prohibited and may be unlawful. 
Please notify the sender immediately. The content of this email is not legally 
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[galaxy-dev] Better descriptions in job history?

[Smithies, Russell]

Not sure if I've overlooked a setting somewhere, but is it possible to 
customize or tweak the job descriptions that are displayed in the history?
Eg. "Compute sequence length on data 1" isn't very descriptive, but if perhaps 
the annotation field or a description field could be added it would make 
identification much easier eg. "Compute sequence length on data 1 [Burkholderia 
pseudomallei K96243]" or even for datatypes that have a defined definition 
line, perhaps a mouse-over hover could be added with the accession or 
definition pulled from the input file? These mouse-over hovers are already used 
to identify the view, edit, and delete icons so no additional libraries wold be 
used.
I could probably hack something up but thought it better to try and get the 
feature included.
Any thoughts?

Thanx,

--Russell
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[galaxy-dev] Managing large database lists in tool wrappers?

[Smithies, Russell]

Does anyone have a workable solution to managing and displaying large lists in 
tool wrappers?
eg.  a database list containing hundreds of enteries in the blast+ tool? (we 
have 1,056 different blast databases).
As a work-around we've split our blast databases into species (eg cow, sheep, 
fungus, clover, fish, rice, etc)  then faked a multi-select to pull in those 
sub-database files with conditional selectors like this:

  

  Pub Databases
  Cattle Databases
  Sheep Databases
  Deer Databases
  Ruminant Databases
  Dog Databases
  Fungi Databases
  Invertebrates Databases
  Microarrays Databases
  Marsupials Databases
  Rodent Databases
  Viruses Databases
  Human Databases
  Microarrays Databases





  
  
  









  
  
  






We end up with a lot of duplication between tool wrappers (I've never managed 
to get an  tag working)  and these aren't exactly simple to maintain 
so does anyone have a better solution?
I had thought about tacking an extra field onto the .loc files with a "species" 
and doing some grouping with that but haven't progressed that idea very far yet.

Any suggestions greatly appreciated :)

Thanx,

--Russell
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Re: [galaxy-dev] Managing large database lists in tool wrappers?

[Smithies, Russell]

Hi Bjoern,
Yes I'm aware of the macros but I've never managed to get them to work ;-(

What I'd like is something like a php include tag to pull the contents of a 
whole file into another file so I'm not repeating myself eg. for the database 
lists in the megablast, blastn, and tblastn wrappers.  

Those select fields are nice, and in "ordinary" html and JQuery you can do 
grouping but as far as I can tell it's not possible with Galaxy/Cheetah XML 
templating - though we are a few versions behind so may have overlooked recent 
updates.

Thanx for your suggestions,

--Russell

-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Björn Grüning
Sent: Tuesday, 1 April 2014 10:19 a.m.
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Managing large database lists in tool wrappers?

Hi Russell,

would something like a http://ivaynberg.github.io/select2/ field work for you?
What do you mean with  tags? Are you aware of Galaxy macros? 
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML_Macros

Cheers,
Bjoern

Am 31.03.2014 22:58, schrieb Smithies, Russell:
> Does anyone have a workable solution to managing and displaying large lists 
> in tool wrappers?
> eg.  a database list containing hundreds of enteries in the blast+ tool? (we 
> have 1,056 different blast databases).
> As a work-around we've split our blast databases into species (eg cow, sheep, 
> fungus, clover, fish, rice, etc)  then faked a multi-select to pull in those 
> sub-database files with conditional selectors like this:
>
>
>  
>Pub Databases
>Cattle Databases
>Sheep Databases
>Deer Databases
>Ruminant Databases
>Dog Databases
>Fungi Databases
>Invertebrates Databases
>Microarrays Databases
>Marsupials Databases
>Rodent Databases
>Viruses Databases
>Human Databases
>Microarrays Databases
>  
>
>  
>  
>  
>
>
>
>  
>  
>  
>  
>
>
>  
>  
>  
>
>
>
>  
>  
>  
>  
>
>
> We end up with a lot of duplication between tool wrappers (I've never managed 
> to get an  tag working)  and these aren't exactly simple to maintain 
> so does anyone have a better solution?
> I had thought about tacking an extra field onto the .loc files with a 
> "species" and doing some grouping with that but haven't progressed that idea 
> very far yet.
>
> Any suggestions greatly appreciated :)
>
> Thanx,
>
> --Russell
>
>
>
> ___
> 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: [galaxy-dev] Managing large database lists in tool wrappers?

[Smithies, Russell]

Those macros look great and are exactly what I want :-)

Thanx,

--Russell

-Original Message-
From: Björn Grüning [mailto:bjoern.gruen...@gmail.com] 
Sent: Tuesday, 1 April 2014 11:07 a.m.
To: Smithies, Russell; Björn Grüning; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Managing large database lists in tool wrappers?

Hi Russell,

Am 31.03.2014 23:46, schrieb Smithies, Russell:
> Hi Bjoern,
> Yes I'm aware of the macros but I've never managed to get them to work 
> ;-(

Lets try to get them to work. It will do exactly what you want.
The Homer Tools should be a easy enough to get you started:

https://github.com/bgruening/galaxytools/tree/master/homer/tools


> What I'd like is something like a php include tag to pull the contents of a 
> whole file into another file so I'm not repeating myself eg. for the database 
> lists in the megablast, blastn, and tblastn wrappers.
>
> Those select fields are nice, and in "ordinary" html and JQuery you 
> can do grouping but as far as I can tell it's not possible with 
> Galaxy/Cheetah XML templating - though we are a few versions behind so may 
> have overlooked recent updates.

Not yet, but I think it would be easy to implement it. It's used in other areas 
of Galaxy a lot.

Ciao,
Bjoern

> Thanx for your suggestions,
>
> --Russell
>
> -Original Message-
> From: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Björn 
> Grüning
> Sent: Tuesday, 1 April 2014 10:19 a.m.
> To: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Managing large database lists in tool wrappers?
>
> Hi Russell,
>
> would something like a http://ivaynberg.github.io/select2/ field work for you?
> What do you mean with  tags? Are you aware of Galaxy macros?
> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML
> _Macros
>
> Cheers,
> Bjoern
>
> Am 31.03.2014 22:58, schrieb Smithies, Russell:
>> Does anyone have a workable solution to managing and displaying large lists 
>> in tool wrappers?
>> eg.  a database list containing hundreds of enteries in the blast+ tool? (we 
>> have 1,056 different blast databases).
>> As a work-around we've split our blast databases into species (eg cow, 
>> sheep, fungus, clover, fish, rice, etc)  then faked a multi-select to pull 
>> in those sub-database files with conditional selectors like this:
>>
>> 
>>   
>> Pub Databases
>> Cattle Databases
>> Sheep Databases
>> Deer Databases
>> Ruminant Databases
>> Dog Databases
>> Fungi Databases
>> Invertebrates Databases
>> Microarrays Databases
>> Marsupials Databases
>> Rodent Databases
>> Viruses Databases
>> Human Databases
>> Microarrays Databases
>>   
>>
>>   
>>   
>>   
>> 
>> 
>> 
>>   
>>   
>>   
>>   
>>
>>
>>   
>>   
>>   
>> 
>> 
>> 
>>   
>>   
>>   
>>   
>>
>>
>> We end up with a lot of duplication between tool wrappers (I've never 
>> managed to get an  tag working)  and these aren't exactly simple to 
>> maintain so does anyone have a better solution?
>> I had thought about tacking an extra field onto the .loc files with a 
>> "species" and doing some grouping with that but haven't progressed that idea 
>> very far yet.
>>
>> Any suggestions greatly appreciated :)
>>
>> Thanx,
>>
>> --Russell
>>
>>
>>
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[galaxy-dev] Custom Cheetah filters?

[Smithies, Russell]

I want to add a filter to strip whitespace and newlines from a text input box 
so I can pipe the sanitized string to a command.
Documentation is a bit sparse (and my Python a bit basic) so does anyone have 
an example?
Perhaps there's a better way of doing it - regex maybe?

Any ideas?

Thanx,

--Russell
--


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Re: [galaxy-dev] Fwd: Custom Cheetah filters?

[Smithies, Russell]

Bodged using string functions :-)

set $data = ''.join([line for line in ($seq_source_type.seq_paste.split()) if 
line[0] != ">"])

Removes the fasta header line and any white-space so I can pipe sequence 
directly to blastn.
Means users can quickly paste in a bit of sequence for blasting without first 
having to upload the data to their history.

--Russell
--

From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Ross
Sent: Wednesday, 13 February 2013 1:34 p.m.
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Fwd: Custom Cheetah filters?

Hi Russell,

There may be a better way, but this works for me in the Toolfactory to create 
space and special character free names?



 



On Wed, Feb 13, 2013 at 11:22 AM, Smithies, Russell 
mailto:russell.smith...@agresearch.co.nz>> 
wrote:
I want to add a filter to strip whitespace and newlines from a text input box 
so I can pipe the sanitized string to a command.
Documentation is a bit sparse (and my Python a bit basic) so does anyone have 
an example?
Perhaps there's a better way of doing it - regex maybe?

Any ideas?

Thanx,

--Russell
--


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[galaxy-dev] dynamic select problem

[Smithies, Russell]

I've been tweaking the blast+ tool xml to simplify database selection for our 
users (we have a lot of databases) and have made it multi-tiered through the 
use of two select boxen and a filter.
Basically, I've added an extra column to blastdb.loc with a group name, then 
use this as a filter to only display the group of databases that were chosen in 
the top select. 
Surprisingly it works - but I doubt it was the intention of the devs who wrote 
the filter code!

But there's a small bug that I can't see, the selects work correctly but I get 
a warning on the secondary one "An invalid option was selected, please verify"
Any ideas what I've overlooked?

Ideally I'd like to only read the file once and load into a data structure then 
populate the second select based on the choice from the top one - but that may 
be asking too much from Cheetah and Galaxy?

Thanx,

--Russell


My select code looks like this:



   
   
   
   
  








  



This is an example of the extra column added to blastdb.loc:

agall.seq   All AgResearch ESTs 
/dataset/blastdata/active/species/agall.seq AgR Databases
agruminant_plus.seq All AgResearch Ruminant ESTs, plus NCBI public Bos 
Taurus as at 3/2002, plus NCBI Sheep at 7/2002   
/dataset/blastdata/active/species/agruminant_plus.seq  Ruminant Databases
galaxy-dev@inconstant$ head -n20 ../../tool-data/blastdb.loc.4col
arrayprinturg15k.seq15Kurg (ESTs)   
/dataset/blastdata/active/species/arrayprinturg15k.seq  Microarray Databases
454AllContigs.fna   454 Seqs 20/5/2007   
/dataset/blastdata/active/species/454AllContigs.fna Sheep Databases
AffyBovineArray052006.seq   Affy Bovine Array at 5/2006 
/dataset/blastdata/active/species/AffyBovineArray052006.seq Cattle Databases
AFT_Affy_chip_seqs.fa   AFT Affy Array 6/2006   
/dataset/blastdata/active/species/AFT_Affy_chip_seqs.fa Fungal Databases
agilent_mouse   Agilent Mouse Array 012694 (as at 2/2007)   
/dataset/blastdata/active/species/agilent_mouse Rodent Databases
est all public ESTs /dataset/blastdata/active/species/est   Pub 
Databases
est_others  all "other" public ESTs (other than Human Databases, mouse) 
/dataset/blastdata/active/species/est_othersPub Databases
agall_plus.seq  All AgResearch ESTs, plus NCBI public Bos Taurus as at 3/2002, 
plus NCBI Sheep at 7/2002
/dataset/blastdata/active/species/agall_plus.seq  AgR Databases
agall.seq   All AgResearch ESTs 
/dataset/blastdata/active/species/agall.seq AgR Databases
agruminant_plus.seq All AgResearch Ruminant ESTs, plus NCBI public Bos 
Taurus as at 3/2002, plus NCBI Sheep at 7/2002   
/dataset/blastdata/active/species/agruminant_plus.seq  Ruminant Databases
agruminant.seq  All AgResearch Ruminant ESTs
/dataset/blastdata/active/species/agruminant.seqRuminant Databases
build2_allssr.seq   All BT2.0 SSRs  
/dataset/blastdata/active/species/build2_allssr.seq Cattle Databases
Allium_cepa Allium cepa DFCI gene indices   
/dataset/blastdata/active/species/Allium_cepa   Plant Databases
angrep.ref  angrep.ref  /dataset/blastdata/active/species/angrep.ref
Repeat Databases
fungalnucs_AR3018_454   AR3018 454 reads, trimmed, 12/2009  
/dataset/blastdata/active/species/fungalnucs_AR3018_454 Fungal Databases
fungalnucs_AR3018_454ContigsNewbler2.0  AR3018 454 build, 12/2009   
/dataset/blastdata/active/species/fungalnucs_AR3018_454ContigsNewbler2.0
Fungal Databases


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