January 2010 - galaxy-dev - lists.galaxyproject.org

Another slowness question
by Assaf Gordon 21 Jan '10

21 Jan '10

Me again, my Galaxy server is still slow, and I'm desperately looking for possible solutions. Any help, suggestion or idea (from anyone) will be highly appreciated. The metadata is now set externally. The database is postgres, switching to MySql showed minor improvement (especially after reboot, where all cache was probably used by MySQL). The python process goes to %40 while few jobs are running, and goes to 100% when a lot of jobs are running and a lot of users accessing galaxy (list their histories, run tools, workflows, etc.). One strange thing that I'm seeing, is that the python process never goes above 100% (actually 106% but I suspect some 'top' summing inaccuracies). Enabling threads-view in top (pressing 'H') shows all the python threads, but their CPU usage *always* sums up to 100% - never higher. I would assume that a true multi-threaded application can easily go above 100% - each thread should be able to reach 100% independently. Could it be a problem in my python installation ? maybe it doesn't support threads correctly ? or is this a wild goose chase? Thanks, -gordon

4 9

custom file type and files in a folder
by Chung Tae-Hoon 21 Jan '10

21 Jan '10

Hi, All I have two questions. If I want to use unsupported custom file types, what steps do I need to follow? Also, if I want to use all/some files in a folder, how can I do that? I think it would be really nice if galaxy can allow importing third party file types / data types / other options in totally separate source trees from original source tree. TH

2 1

Database creation errors with MySQL 5.0
by Assaf Gordon 20 Jan '10

20 Jan '10

Hello, When running galaxy for the first time (sh run.sh) and connecting to a MySQL 5.0 server, the following errors happen: =============== 0010_hda_display_at_authz_table DEBUG 2010-01-19 14:49:37,695 Creating history_dataset_association_display_at_authorization table failed: (OperationalError) (1059, "Identifier name 'ix_history_dataset_association_display_at_authorization_update_time' is too long") u'CREATE INDEX ix_history_dataset_association_display_at_authorization_update_time ON history_dataset_association_display_at_authorization (update_time)' () 0013_change_lib_item_templates_to_forms DEBUG 2010-01-19 14:50:12,272 Creating library_dataset_dataset_info_association table failed: (OperationalError) (1059, "Identifier name 'ix_library_dataset_dataset_info_association_library_dataset_dataset_association_id' is too long") u'CREATE INDEX ix_library_dataset_dataset_info_association_library_dataset_dataset_association_id ON library_dataset_dataset_info_association (library_dataset_dataset_association_id)' () 0015_tagging DEBUG 2010-01-19 14:50:53,975 Creating history_dataset_association_tag_association table failed: (OperationalError) (1059, "Identifier name 'ix_history_dataset_association_tag_association_history_dataset_association_id' is too long") u'CREATE INDEX ix_history_dataset_association_tag_association_history_dataset_association_id ON history_dataset_association_tag_association (history_dataset_association_id)' () 0017_library_item_indexes DEBUG 2010-01-19 14:50:56,813 Adding index 'ix_library_folder_name' to library_folder table failed: (OperationalError) (1170, "BLOB/TEXT column 'name' used in key specification without a key length") 'CREATE INDEX ix_library_folder_name ON library_folder (name)' () ===================== Three of them (10,13,15) happen because the auto-generated key name (based on the table's name and column) is too long. The other (17) is because in MySQL, creating an index on a "Text" field requires a length (index on VARCHAR doesn't require it). The current workaround is to create these indices manually. While MySQL 5.0 is a bit too old, it is still the standard version on debian/stable and CentOS 5.4, so I have to use it. -gordon

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Re: [galaxy-dev] [galaxy-user] Tool without input parameters
by Assaf Gordon 18 Jan '10

18 Jan '10

Or just add a dummy input parameter, like so: ========= <inputs> <param name="dummy" type="text" label="Don't touch me" /> </inputs> <outputs> <data format="html" name="output" /> </outputs> ========= It looks silly, but it works just fine (we have couple of tools like that ;) ). -gordon Gunnar Raetsch wrote, On 01/15/2010 07:49 AM: > Hi, > > that would be indeed a useful feature... > > What I did some time ago is to let the user choose some example data > (e.g. for different organisms), that will be generated into the history. > > Then you have some input, outputs and can write the overview in the > tool description. > > Cheers, Gunnar > > > On 15.01.2010, at 13:06, Jelle Scholtalbers wrote: > >> Hi, >> >> Is there a way to provide a tool through galaxy that doesn't need any >> input parameters? If I just don't specify a parameter I get an error: >> "AttributeError: Tool instance has no attribute 'inputs'" >> Specifying a hidden input parameter will load the xml, but in galaxy >> it won't show a tool overview or execute the tool for you when you >> click on its name. >> >> Cheers, >> Jelle >> >> _______________________________________________ >> galaxy-user mailing list >> galaxy-user(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-user > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

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Re: [galaxy-dev] [galaxy-bugs] Galaxy tool error report from csilhah@nus.edu.sg
by Kelly Vincent 15 Jan '10

15 Jan '10

Hi Luqman, From your description, it sounds like everything was set up correctly, so I don't immediately know what went wrong. Could you share your history with me (kpvincent(a)bx.psu.edu)? Then I will be able to look into this in more detail. (To share your history, click on Options in the History pane and choose Share. You can enter the email here.) Regards, Kelly On Wed 13 Jan 2010, at 4:07 AM, galaxy-bugs(a)bx.psu.edu wrote: > > GALAXY TOOL ERROR REPORT > ------------------------ > > This error report was sent from the Galaxy instance hosted on the > server > "main.g2.bx.psu.edu" > ----------------------------------------------------------------------------- > This is in reference to dataset id 999375 from history id 312707 > ----------------------------------------------------------------------------- > You should be able to view the history containing the related > history item > > 3: Map with Bowtie on data 2 > > by logging in as a Galaxy admin user to the Galaxy instance > referenced above > and pointing your browser to the following link. > > main.g2.bx.psu.edu/history/view?id=e11c642116fd76eb > ----------------------------------------------------------------------------- > The user 'csilhah(a)nus.edu.sg' provided the following information: > > Hi there, > > Im having trouble running bowtie as you can see. Heres what i did: > > 1. I get example_sequence.txt file from my Illumina run. This is > supposedly a fastq file (using the > 1.3 version). > > 2. I use FASTQ Groomer to convert it into fastqsanger format, > bearing in mind to put the option as converting from Illumina 1.3 > format. > > 3. Use output from 2. to align to hg19 on Bowtie. > > Help is greatly appreciated! > > Luqman > ----------------------------------------------------------------------------- > job id: 779082 > tool id: bowtie_wrapper > ----------------------------------------------------------------------------- > job command line: > python /galaxy/home/g2main/galaxy_main/tools/sr_mapping/ > bowtie_wrapper.py --threads="4" --input1=/galaxy/home/ > g2main/galaxy_main/database/files/000/999/dataset_999372.dat -- > input2="None" --output=/galaxy/home/g2main/galaxy_main/database/ > tmp/job_working_directory/779082/galaxy_dataset_999375.dat -- > paired=single --genomeSource=indexed --ref=/depot/data2/ > galaxy/hg19/bowtie_index/hg19 --params=pre_set -- > skip="None" --alignLimit="None" --trimH="None" -- > trimL="None" --mismatchSeed="None" -- > mismatchQual="None" --seedLen="None" -- > rounding="None" --maqSoapAlign="None" -- > tryHard="None" --valAlign="None" -- > allValAligns="None" --suppressAlign="None" -- > best="None" --maxBacktracks="None" --strata="None" -- > minInsert="None" --maxInsert="None" -- > mateOrient="None" --maxAlignAttempt="None" -- > forwardAlign="None" --reverseAlign="None" --offrate="Non > e" --seed="None" --dbkey="None" -- > indexSettings="None" --iauto_b="None" -- > ipacked="None" --ibmax="None" --ibmaxdivn="None" -- > idcv="None" --inodc="None" --inoref="None" -- > ioffrate="None" --iftab="None" --intoa="None" -- > iendian="None" --iseed="None" --icutoff="None" -- > suppressHeader=true > ----------------------------------------------------------------------------- > job stderr: > sh: line 1: 6372 Aborted bowtie -p 4 -S /depot/ > data2/galaxy/hg19/bowtie_index/hg19 /galaxy/home/g2main/galaxy_main/ > database/files/000/999/dataset_999372.dat > /galaxy/home/g2main/ > galaxy_main/database/tmp/job_working_directory/779082/ > galaxy_dataset_999375.dat 2> /dev/null > > ----------------------------------------------------------------------------- > job stdout: > > ----------------------------------------------------------------------------- > job info: > None > ----------------------------------------------------------------------------- > job traceback: > None > ----------------------------------------------------------------------------- > (This is an automated message). > _______________________________________________ > galaxy-bugs mailing list > galaxy-bugs(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-bugs

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Apache proxy configs - still..
by Kimberly Begley 15 Jan '10

15 Jan '10

Hello, Just a quick update - I'm still having problems - I have tested out the remote_user variable setting with a php script and it is being set to the email address entered in the LDAP authentication page but Galaxy is giving me the error: Access to Galaxy is denied Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server. Please contact your local Galaxy administrator. Any ideas? Thanks, Kimberly On Tue, Dec 22, 2009 at 6:30 AM, <galaxy-dev-request(a)lists.bx.psu.edu>wrote: > Send galaxy-dev mailing list submissions to > galaxy-dev(a)lists.bx.psu.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.bx.psu.edu/listinfo/galaxy-dev > or, via email, send a message with subject or body 'help' to > galaxy-dev-request(a)lists.bx.psu.edu > > You can reach the person managing the list at > galaxy-dev-owner(a)lists.bx.psu.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-dev digest..." > > > Today's Topics: > > 1. Re: Apache proxy configs (Nate Coraor) > 2. Re: Apache proxy configs (Kimberly Begley) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 21 Dec 2009 12:35:40 -0500 > From: Nate Coraor <nate(a)bx.psu.edu> > To: Kimberly Begley <kimberly(a)fisciconsulting.com> > Cc: galaxy-dev(a)bx.psu.edu > Subject: Re: [galaxy-dev] Apache proxy configs > Message-ID: <4B2FB1EC.9090304(a)bx.psu.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Have you tried it with your working URL? It looks like it returns a > full email: > > AuthLDAPURL > ldap://servername.part1.part2.edu:389/dc=part1,dc=part2,dc=edu?mail > RequestHeader set REMOTE_USER %{AUTHENTICATE_mail}e > > --nate > > Kimberly Begley wrote: > > Hello - sorry not enough details - was trying to get an idea if I was > > missing another chunk of settings. Server name has been adjusted. > > > > This is what we have set up for general authentication on the machine > > and it works fine. > > > >> <Directory /> > >> Options FollowSymLinks > >> AllowOverride None > >> > >> AuthName " LDAP Test Web Site" > >> AuthType Basic > >> AuthBasicProvider ldap > >> AuthzLDAPAuthoritative off > >> AuthLDAPURL > >> ldap://servername.part1.part2.edu:389/dc=part1,dc=part2,dc=edu?mail > >> Require valid-user > >> </Directory> > >> > >> > >> OK - instructions say do this: > >> > >> <Location /> > >> AuthType Basic > >> AuthBasicProvider ldap > >> AuthLDAPURL > >> > "ldap://server:389/ou=People,dc=example,dc=org?uid?sub?(objectClass=person)" > >> AuthzLDAPAuthoritative off > >> Require valid-user > >> </Location> > >> RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e > >> > >> > >> If I do this: > >> > >> Directory /> > >> Options FollowSymLinks > >> AllowOverride None > >> > >> AuthName " LDAP Test Web Site" > >> AuthType Basic > >> AuthBasicProvider ldap > >> AuthzLDAPAuthoritative off > >> > >> AuthLDAPURL > >> "ldap:// > servername.part1.part2.edu:389/ou=People,dc=part1,dc=part2,dc=edu?uid?sub?(objectClass=person)<http://servername.part1.part2.edu:389/ou=People,dc=part1,dc=part2,dc=edu?ui…> > " > >> Require valid-user > >> </Directory> > >> RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e > >> > >> > >> gives (in the http error log) from trying to open the sample page....: > >> > >> Thu Dec 17 22:43:22 2009] [warn] [client ] [7281] auth_ldap > >> authenticate: user kimberly(a)host.net > >> <mailto:kimberly@host.net> authentication failed; URI / [User not > found][No > >> such object] > >> [Thu Dec 17 22:43:22 2009] [error] [client ] user kimberly(a)host.net > >> <mailto:kimberly@host.net <ann(a)host.net>> not found: / > >> [Thu Dec 17 22:43:31 2009] [warn] [client ] [7282] auth_ldap > >> authenticate: user kimberly(a)host.net > >> <mailto:kimberly@host.net <ann(a)host.net>> authentication failed; URI / > [User not found][No > >> such object] > >> [Thu Dec 17 22:43:31 2009] [error] [client ] user kimberly(a)host.net > >> <mailto:kimberly@host.net <ann(a)host.net>> not found: / > >> > >> > >> > >> If I change it so that we omit the uid reference to make it a mail > >> reference like this: > >> > >> Directory /> > >> Options FollowSymLinks > >> AllowOverride None > >> > >> AuthName "hpc108 LDAP Test Web Site" > >> AuthType Basic > >> AuthBasicProvider ldap > >> AuthzLDAPAuthoritative off > >> AuthLDAPURL > >> "ldap:// > servername.part1.part2.edu:389/ou=People,dc=part1,dc=part2,dc=edu?mail?sub?(objectClass=person)<http://servername.part1.part2.edu:389/ou=People,dc=part1,dc=part2,dc=edu?ma…> > " > >> Require valid-user > >> </Directory> > >> RequestHeader set REMOTE_USER %{AUTHENTICATE_mail}e > >> > >> The sample page connects but the galaxy page says the REMOTE_USER is > >> empty like this: > >> > >> Access to Galaxy is denied > >> > >> Galaxy is configured to authenticate users via an external method > >> (such as HTTP authentication in Apache), but a username was not > >> provided by the upstream (proxy) server. This is generally due to a > >> misconfiguration in the upstream server. > >> > >> Please contact your local Galaxy administrator. > >> > >> > >> > >> Then if I change it up a bit and keep the URL line with the mail > >> reference and change the request header to the uid reference - the > >> sample page loads but the galaxy page gives the above access denied > >> message and these messages in the galaxy log: > >> > >> > >> > >> > >> 10.1.74.61 - - [17/Dec/2009:22:59:08 -0400] "GET /galaxy_test/ > >> HTTP/1.1" 403 - "-" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_5_8; > >> en-us) AppleWebKit/531.21.8 (KHTML, like Gecko) Version/4.0.4 > >> Safari/531.21.10" > >> > >> 10.1.74.61 - - [17/Dec/2009:22:59:22 -0400] "GET /galaxy_test/ > >> HTTP/1.1" 403 - "-" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_5_8; > >> en-us) AppleWebKit/531.21.8 (KHTML, like Gecko) Version/4.0.4 > >> Safari/531.21.10" > >> > >> > >> > >> > >> I have also tried a zillion combinations with the ou, dc and sub tags > >> to no avail - but I might have missed the one combination that works! > >> > >> Just putting this out there in case it is obvious to you guys where > >> the problem may be..... > > > > Any ideas? > > > > Thanks in advance, > > > > Kimberly > > > >> > > On 19/12/2009, at 1:54 AM, Nate Coraor wrote: > > > >> Kimberly Begley wrote: > >> > >>> I am trying to set up the apache proxy setting for a local galaxy > >>> install. > >>> I have this section set but the REMOTE_USER is not getting set > properly: > >>> <Location /> > >>> AuthType Basic > >>> AuthBasicProvider ldap > >>> AuthLDAPURL > >>> > "ldap://server:389/ou=People,dc=domain,dc=edu?uid?sub?(objectClass=person)" > >>> AuthzLDAPAuthoritative off > >>> Require valid-user > >>> </Location> > >>> RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e > >>> I have a feeling I'm missing something. > >>> The authentication for the server is working but the galaxy interface > >>> gives the error message that the remote user is not being sent. > >>> Any additional settings that I'm missing here? > >> > >> Hi Kimberly, > >> > >> If you're using that exact block, it would not work. Your AuthLDAPURL > >> value will need to be modified to your site. This normally means > >> changing: > >> > >> "ldap://" to "ldaps://" if using LDAP over SSL. > >> "server" to the hostname of your LDAP server. > >> "389" to an alternate port if applicable. > >> "ou=People" to another organizational unit if your user accounts live > >> at a different location in the LDAP directory (although "People" is > >> the standard) > >> "dc=domain,dc=edu" to the base distinguished name used by your LDAP > >> server (usually, but not always, your DNS domain) > >> "uid" to the LDAP field containing the user name. > >> "person" to one of the object classes assigned to account entries. > >> > >> This requires a pretty substantial knowledge of LDAP, so if unsure, > >> it'd be best to contact your LDAP directory administrator. > >> > >> --nate > > > > Kimberly Begley | Bioinformatician, Project Manager > > Tel: +61 7 3371 6554 | Mobile: 0422 393 833 > > Email: kimberly(a)fisciconsulting.com > > <mailto:kimberly@fisciconsulting.com> Web: www.fisciconsulting.com > > <http://www.fisciconsulting.com> > > 91/59 Keating St, Indooroopilly QLD 4068 Australia > > > > > > -------------- > > If you are not the authorized recipient of this email please contact > > Finance Science Consulting by return email or telephone at +61 7 5545 > > 4761. In this case you must delete document and not use or disclose the > > information and/or copyright material of Finance Science Consulting. > > Finance Science Consulting states that any opinions expressed in this > > email are those of the individual sender and should not be taken as > > representative of the views of the Company. > > > > > > > > > > > > > > > > > > ------------------------------ > > Message: 2 > Date: Tue, 22 Dec 2009 06:04:56 +1000 > From: Kimberly Begley <kimberly(a)fisciconsulting.com> > To: Nate Coraor <nate(a)bx.psu.edu> > Cc: galaxy-dev(a)bx.psu.edu > Subject: Re: [galaxy-dev] Apache proxy configs > Message-ID: <B3487D90-DDC2-4DDB-A281-A625BFB058B7(a)fisciconsulting.com> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > Hi Nate, > > Yes - it works fine for the sample ldap page but gives the same galaxy > message on screen: > > Access to Galaxy is denied > > Galaxy is configured to authenticate users via an external method > (such as HTTP authentication in Apache), but a username was not > provided by the upstream (proxy) server. This is generally due to a > misconfiguration in the upstream server. > > Please contact your local Galaxy administrator. > > > > Galaxy log says: > > 21/Dec/2009:15:00:22 -0400] "GET /galaxy_test/ HTTP/1.1" 403 - "-" > "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_5_8; en-us) AppleWebKit/ > 531.21.8 (KHTML, like Gecko) Version/4.0.4 Safari/531.21.10" > > > Thanks, > Kimberly > > On 22/12/2009, at 3:35 AM, Nate Coraor wrote: > > > Have you tried it with your working URL? It looks like it returns a > > full email: > > > > AuthLDAPURL ldap://servername.part1.part2.edu:389/ > > dc=part1,dc=part2,dc=edu?mail > > RequestHeader set REMOTE_USER %{AUTHENTICATE_mail}e > > > > --nate > > > > Kimberly Begley wrote: > >> Hello - sorry not enough details - was trying to get an idea if I > >> was missing another chunk of settings. Server name has been adjusted. > >> This is what we have set up for general authentication on the > >> machine and it works fine. > >>> <Directory /> > >>> Options FollowSymLinks > >>> AllowOverride None > >>> > >>> AuthName " LDAP Test Web Site" > >>> AuthType Basic > >>> AuthBasicProvider ldap > >>> AuthzLDAPAuthoritative off > >>> AuthLDAPURL ldap://servername.part1.part2.edu:389/ > >>> dc=part1,dc=part2,dc=edu?mail > >>> Require valid-user > >>> </Directory> > >>> > >>> > >>> OK - instructions say do this: > >>> > >>> <Location /> > >>> AuthType Basic > >>> AuthBasicProvider ldap > >>> AuthLDAPURL "ldap://server:389/ou=People,dc=example,dc=org?uid? > >>> sub?(objectClass=person)" > >>> AuthzLDAPAuthoritative off > >>> Require valid-user > >>> </Location> > >>> RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e > >>> > >>> > >>> If I do this: > >>> > >>> Directory /> > >>> Options FollowSymLinks > >>> AllowOverride None > >>> > >>> AuthName " LDAP Test Web Site" > >>> AuthType Basic > >>> AuthBasicProvider ldap > >>> AuthzLDAPAuthoritative off > >>> > >>> AuthLDAPURL "ldap://servername.part1.part2.edu:389/ > >>> ou=People,dc=part1,dc=part2,dc=edu?uid?sub?(objectClass=person)" > >>> Require valid-user > >>> </Directory> > >>> RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e > >>> > >>> > >>> gives (in the http error log) from trying to open the sample > >>> page....: > >>> > >>> Thu Dec 17 22:43:22 2009] [warn] [client ] [7281] auth_ldap > >>> authenticate: user kimberly(a)host.net <mailto:kimberly@host.net<ann(a)host.net> > > > >>> authentication failed; URI / [User not found][No such object] > >>> [Thu Dec 17 22:43:22 2009] [error] [client ] user > >>> kimberly(a)host.net <mailto:kimberly@host.net <ann(a)host.net>> not found: > / > >>> [Thu Dec 17 22:43:31 2009] [warn] [client ] [7282] auth_ldap > >>> authenticate: user kimberly(a)host.net <mailto:kimberly@host.net<ann(a)host.net> > > > >>> authentication failed; URI / [User not found][No such object] > >>> [Thu Dec 17 22:43:31 2009] [error] [client ] user > >>> kimberly(a)host.net <mailto:kimberly@host.net <ann(a)host.net>> not found: > / > >>> > >>> > >>> > >>> If I change it so that we omit the uid reference to make it a mail > >>> reference like this: > >>> > >>> Directory /> > >>> Options FollowSymLinks > >>> AllowOverride None > >>> > >>> AuthName "hpc108 LDAP Test Web Site" > >>> AuthType Basic > >>> AuthBasicProvider ldap > >>> AuthzLDAPAuthoritative off > >>> AuthLDAPURL "ldap://servername.part1.part2.edu:389/ > >>> ou=People,dc=part1,dc=part2,dc=edu?mail?sub?(objectClass=person)" > >>> Require valid-user > >>> </Directory> > >>> RequestHeader set REMOTE_USER %{AUTHENTICATE_mail}e > >>> > >>> The sample page connects but the galaxy page says the REMOTE_USER > >>> is empty like this: > >>> > >>> Access to Galaxy is denied > >>> > >>> Galaxy is configured to authenticate users via an external method > >>> (such as HTTP authentication in Apache), but a username was not > >>> provided by the upstream (proxy) server. This is generally due to > >>> a misconfiguration in the upstream server. > >>> > >>> Please contact your local Galaxy administrator. > >>> > >>> > >>> > >>> Then if I change it up a bit and keep the URL line with the mail > >>> reference and change the request header to the uid reference - the > >>> sample page loads but the galaxy page gives the above access > >>> denied message and these messages in the galaxy log: > >>> > >>> > >>> > >>> > >>> 10.1.74.61 - - [17/Dec/2009:22:59:08 -0400] "GET /galaxy_test/ > >>> HTTP/1.1" 403 - "-" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X > >>> 10_5_8; en-us) AppleWebKit/531.21.8 (KHTML, like Gecko) Version/ > >>> 4.0.4 Safari/531.21.10" > >>> > >>> 10.1.74.61 - - [17/Dec/2009:22:59:22 -0400] "GET /galaxy_test/ > >>> HTTP/1.1" 403 - "-" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X > >>> 10_5_8; en-us) AppleWebKit/531.21.8 (KHTML, like Gecko) Version/ > >>> 4.0.4 Safari/531.21.10" > >>> > >>> > >>> > >>> > >>> I have also tried a zillion combinations with the ou, dc and sub > >>> tags to no avail - but I might have missed the one combination > >>> that works! > >>> > >>> Just putting this out there in case it is obvious to you guys > >>> where the problem may be..... > >> Any ideas? > >> Thanks in advance, > >> Kimberly > >>> > >> On 19/12/2009, at 1:54 AM, Nate Coraor wrote: > >>> Kimberly Begley wrote: > >>> > >>>> I am trying to set up the apache proxy setting for a local galaxy > >>>> install. > >>>> I have this section set but the REMOTE_USER is not getting set > >>>> properly: > >>>> <Location /> > >>>> AuthType Basic > >>>> AuthBasicProvider ldap > >>>> AuthLDAPURL "ldap://server:389/ou=People,dc=domain,dc=edu?uid? > >>>> sub?(objectClass=person)" > >>>> AuthzLDAPAuthoritative off > >>>> Require valid-user > >>>> </Location> > >>>> RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e > >>>> I have a feeling I'm missing something. > >>>> The authentication for the server is working but the galaxy > >>>> interface gives the error message that the remote user is not > >>>> being sent. > >>>> Any additional settings that I'm missing here? > >>> > >>> Hi Kimberly, > >>> > >>> If you're using that exact block, it would not work. Your > >>> AuthLDAPURL value will need to be modified to your site. This > >>> normally means changing: > >>> > >>> "ldap://" to "ldaps://" if using LDAP over SSL. > >>> "server" to the hostname of your LDAP server. > >>> "389" to an alternate port if applicable. > >>> "ou=People" to another organizational unit if your user accounts > >>> live at a different location in the LDAP directory (although > >>> "People" is the standard) > >>> "dc=domain,dc=edu" to the base distinguished name used by your > >>> LDAP server (usually, but not always, your DNS domain) > >>> "uid" to the LDAP field containing the user name. > >>> "person" to one of the object classes assigned to account entries. > >>> > >>> This requires a pretty substantial knowledge of LDAP, so if > >>> unsure, it'd be best to contact your LDAP directory administrator. > >>> > >>> --nate > >> Kimberly Begley | Bioinformatician, Project Manager > >> Tel: +61 7 3371 6554 | Mobile: 0422 393 833 > >> Email: kimberly(a)fisciconsulting.com <mailto: > kimberly(a)fisciconsulting.com > >> > Web: www.fisciconsulting.com <http://www.fisciconsulting.com> > >> 91/59 Keating St, Indooroopilly QLD 4068 Australia > >> -------------- > >> If you are not the authorized recipient of this email please > >> contact Finance Science Consulting by return email or telephone at > >> +61 7 5545 4761. In this case you must delete document and not use > >> or disclose the information and/or copyright material of Finance > >> Science Consulting. Finance Science Consulting states that any > >> opinions expressed in this email are those of the individual sender > >> and should not be taken as representative of the views of the > >> Company. > > > > Kimberly Begley | Bioinformatician, Project Manager > Tel: +61 7 3371 6554 | Mobile: 0422 393 833 > Email: kimberly(a)fisciconsulting.com Web: www.fisciconsulting.com > 91/59 Keating St, Indooroopilly QLD 4068 Australia > > > -------------- > If you are not the authorized recipient of this email please contact > Finance Science Consulting by return email or telephone at +61 7 5545 > 4761. In this case you must delete document and not use or disclose > the information and/or copyright material of Finance Science > Consulting. Finance Science Consulting states that any opinions > expressed in this email are those of the individual sender and should > not be taken as representative of the views of the Company. > > > > > > > >

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datasets metadata
by /fox/ 14 Jan '10

14 Jan '10

Hi list, I've inserted some tools into galaxy. I use it like: - upload file data 1 - execute K-Medoid on data 1 (galaxy produces an output file called "K-Medoid on data 1") Then if I want to plot that data I use another tool of mine. It takes 2 inputs, the kmedoid file and the source file (data 1). So I've to select as input "K-Medoid on data 1" and "data 1" How can I extract "data 1" from "K-Medoid on data 1"? I'd like to select only "K-Medoid on data 1" and it should select automatically "data 1". I think that is possible using metadata but I don't know how Thank you in advance p.s.: sorry for my bad english -- f. "E' in un giorno di pioggia che ti ho conosciuta e il vento dell'ovest rideva gentile..." (Modena City Ramblers) http://fox.noblogs.org/

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Fwd: python 2.6.2 and galaxy development
by Anton Nekrutenko 14 Jan '10

14 Jan '10

Begin forwarded message: > From: "Richard Rauscher" <rrauscher(a)hmc.psu.edu> > Date: January 12, 2010 12:39:46 PM EST > To: <anton(a)bx.psu.edu> > Subject: python 2.6.2 and galaxy development > > Hi Anton, > I’m trying to write a module for galaxy (my first attempt) – > wondering if you have any experience with using Python 2.6 with it… > Thx, > -Rich > > Richard Rauscher > Director of IT, Biomedical Research & Penn State Cancer Institute > Director, Cancer Biomedical Informatics Core > Penn State University > Hershey, PA > (717) 531-1066 > rrauscher(a)psu.edu > This signature is RFC 3092 compliant. :-) > *****E-Mail Confidentiality Notice***** > This message (including any attachments) contains information > intended for a specific individual(s) and purpose that may be > privileged, confidential or otherwise protected from disclosure > pursuant to applicable law. Any inappropriate use, distribution or > copying of the message is strictly prohibited and may subject you to > criminal or civil penalty. If you have received this transmission > in error, please reply to the sender indicating this error and > delete the transmission from your system immediately. > Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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Crash while attempting to saving bowtie output
by Chris Cole 12 Jan '10

12 Jan '10

Hi, On our local install, we've just enabled bowtie NGS mapping and although the search runs fine and the output is viewable in Galaxy, any attempt to save it brings down the server. The only error in paster.log is: galaxy.datatypes.registry WARNING 2009-12-18 16:32:38,517 unknown mimetype in data factory sam Tried it on large files and small files with the same effect. Trying save as fails with an 'unable to read file error'. Anyone have any ideas? Cheers, Chris

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file read/write strategies
by Dean Snyder 12 Jan '10

12 Jan '10

Complete, end-user control over how and where Galaxy reads and writes files would be particularly useful for dealing with very large files and for integrating Galaxy output into complex, ad hoc external workflows. I have three suggestions: 1. Rename the "Upload File" tool as "Data Source" and allow users to select whether the specified file should be uploaded to "Galaxy" or read in situ. 2. Create a new tool called "Default Data Destination" with which users can specify the default path where all data output is to be written. 3. Add a "Data Destination" field to the page of every tool that writes output to disk, so users can specify, on a tool-by-tool basis, where they want the output to be written. a. If the user has specified a default location via the "Default Data Destination" tool, the field would be pre-filled with this path; b. if not, the field would be blank (or contain "to Galaxy" in disabled text), and Galaxy will write to its write folder, c. unless the user explicitly specifies a new write path in this field for this tool. I am aware of the various, current ways one can specify file handling strategies within Galaxy, but these seem to be too static, too global, and too "subliminal" for the kind of work at hand; something finer- grained, more pervasive, and more explicit seems to be called for. [If implemented, it is clear that these changes would add fragility to the Galaxy history mechanism, but this could be dealt with at multiple levels, including in the UI by issuing warnings and/or offering choices.] Thanks for all your great work on this fine platform for tool integration. (In the words of one of your very knowledgeable "competitors" on seeing Galaxy for the first time, "This is slick!" ) Dean A. Snyder Senior Programmer/Analyst Center for Inherited Disease Research (CIDR) Johns Hopkins School of Medicine Bayview Research Campus 333 Cassell Dr, Triad Bldg, Suite 2000 Baltimore, MD 21224 www.cidr.jhmi.edu cell:717 668-3048 office:410-550-4629

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