[galaxy-dev] Better descriptions in job history?
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 ___ 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/
[galaxy-dev] Managing large database lists in tool wrappers?
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: conditional name=db_opts param name=db_opts_selector type=select label=Nucleotide Database Type option value=pub selected=TruePub Databases/option option value=cattleCattle Databases/option option value=sheepSheep Databases/option option value=deerDeer Databases/option option value=ruminantRuminant Databases/option option value=dogDog Databases/option option value=fungiFungi Databases/option option value=invertebratesInvertebrates Databases/option option value=microarraysMicroarrays Databases/option option value=marsupialsMarsupials Databases/option option value=rodentRodent Databases/option option value=virusesViruses Databases/option option value=humanHuman Databases/option option value=microarraysMicroarrays Databases/option /param when value=ruminant param name=database type=select label=Ruminant Nucleotide BLAST database help= options from_file=blastdb.ruminant.loc column name=value index=0/ column name=name index=1/ column name=path index=2/ /options /param param name=subject type=hidden value= / /when when value=misc param name=database type=select label=Misc Nucleotide BLAST database help= options from_file=blastdb.misc.loc column name=value index=0/ column name=name index=1/ column name=path index=2/ /options /param param name=subject type=hidden value= / /when We end up with a lot of duplication between tool wrappers (I've never managed to get an include 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/
Re: [galaxy-dev] Managing large database lists in tool wrappers?
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 include 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: conditional name=db_opts param name=db_opts_selector type=select label=Nucleotide Database Type option value=pub selected=TruePub Databases/option option value=cattleCattle Databases/option option value=sheepSheep Databases/option option value=deerDeer Databases/option option value=ruminantRuminant Databases/option option value=dogDog Databases/option option value=fungiFungi Databases/option option value=invertebratesInvertebrates Databases/option option value=microarraysMicroarrays Databases/option option value=marsupialsMarsupials Databases/option option value=rodentRodent Databases/option option value=virusesViruses Databases/option option value=humanHuman Databases/option option value=microarraysMicroarrays Databases/option /param when value=ruminant param name=database type=select label=Ruminant Nucleotide BLAST database help= options from_file=blastdb.ruminant.loc column name=value index=0/ column name=name index=1/ column name=path index=2/ /options /param param name=subject type=hidden value= / /when when value=misc param name=database type=select label=Misc Nucleotide BLAST database help= options from_file=blastdb.misc.loc column name=value index=0/ column name=name index=1/ column name=path index=2/ /options /param param name=subject type=hidden value= / /when We end up with a lot of duplication between tool wrappers (I've never managed to get an include 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/ ___ 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
Re: [galaxy-dev] Managing large database lists in tool wrappers?
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 include 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: conditional name=db_opts param name=db_opts_selector type=select label=Nucleotide Database Type option value=pub selected=TruePub Databases/option option value=cattleCattle Databases/option option value=sheepSheep Databases/option option value=deerDeer Databases/option option value=ruminantRuminant Databases/option option value=dogDog Databases/option option value=fungiFungi Databases/option option value=invertebratesInvertebrates Databases/option option value=microarraysMicroarrays Databases/option option value=marsupialsMarsupials Databases/option option value=rodentRodent Databases/option option value=virusesViruses Databases/option option value=humanHuman Databases/option option value=microarraysMicroarrays Databases/option /param when value=ruminant param name=database type=select label=Ruminant Nucleotide BLAST database help= options from_file=blastdb.ruminant.loc column name=value index=0/ column name=name index=1/ column name=path index=2/ /options /param param name=subject type=hidden value= / /when when value=misc param name=database type=select label=Misc Nucleotide BLAST database help= options from_file=blastdb.misc.loc column name=value index=0/ column name=name index=1/ column name=path index=2/ /options /param param name=subject type=hidden value= / /when We end up with a lot of duplication between tool wrappers (I've never managed to get an include 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
[galaxy-dev] Custom Cheetah filters?
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 -- === 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 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] Fwd: Custom Cheetah filters?
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? param name=foo type=text value= label=Foo sanitizer invalid_char= valid initial=string.letters,string.digits/ /sanitizer /param On Wed, Feb 13, 2013 at 11:22 AM, Smithies, Russell russell.smith...@agresearch.co.nzmailto: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 -- === 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 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] Upload local files
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.nzhttp://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.commailto: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 The information contained in this email is intended solely for the addressee. Access to this email by anyone else unauthorized. If you are not the intended recipient, any form of disclosure, reproduction, distribution or any action 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 binding unless confirmed by letter. === 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 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] NTLM auth not passing http_remote_user?
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:
Location /
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
/Location
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'
===
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
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Re: [galaxy-dev] NTLM auth not passing http_remote_user?
If I take the rewrite out of the location 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:
Location /
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
/Location
snip
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
Location block.
Put it in the global configuration file, after the Location 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
===
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.
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Re: [galaxy-dev] NTLM auth not passing http_remote_user?
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 location section or your initial ntlm auth
wil fail.
Location /
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
/Location
--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 location 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:
Location /
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
/Location
snip
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
Location block.
Put it in the global configuration file, after the Location 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
===
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.
===
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Please keep all replies on the list by using reply all
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lists, please use the interface at:
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___
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[galaxy-dev] re-writing username for login or stripping domain from remote_user?
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.nzhttp://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 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 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] 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 === 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 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] scripts in welcome.html?
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 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 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] possibly weird config requests...
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:
Location /galaxy
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
/Location
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
russell.smith...@agresearch.co.nz 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 easier?
The public tool shed or a local tool shed would allow for this. Note that
users
still need administrative privileges to install tools from a tool shed.
--nate
* 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
Re: [galaxy-dev] proxy settings?
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', httplib.HTTPMessage instance at 0x35d2998)
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.
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[galaxy-dev] possibly weird config requests...
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 === 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 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] 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', httplib.HTTPMessage instance at 0x35d2998)
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.
===
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[galaxy-dev] tool for RepeatMasker?
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 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] tool for RepeatMasker?
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 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/
