- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Some plugin for digital normalization
by Michael R. Crusoe 24 Nov '14

24 Nov '14

> From: Cristian Alejandro Rojas <alejandro.0317(a)gmail.com> > Date: December 26, 2013 2:37 AM > To: galaxy-dev(a)lists.bx.psu.edu > Subject: [galaxy-dev] Some plugin for digital normalization > Hello all, > > I've been searching in tool sheds(main and test) for a plugin to do digital normalization of reads, for example Trinity has one script to do this (./util/normalize_by_kmer_coverage.pl), diginorm is another alternative (http://ged.msu.edu/papers/2012-diginorm/) > > Do you know if there is a galaxy tool ready for this work or should I develop my own? Hello Cristian, I am actively working on a wrapper for normalize-by-median.py and the other tools in the khmer suite. https://github.com/ged-lab/khmer/blob/galaxy-integration/scripts/normalize-… It requires some changes on our end which you can track here: https://github.com/ged-lab/khmer/pull/237 You can install this branch of khmer via pip pip install -e git+git@github.com:ged-lab/khmer.git@output_naming1#egg=khmer or if you don't have a github account: pip install -e git+ https://github.com/ged-lab/khmer.git@output_naming1#egg=khmer (Instructions on installing using a virtualenv or on OS X are at: https://khmer.readthedocs.org/en/latest/install.html just substitute in the pertinent pip line from above) I haven't tested it much; doing so is the top of my to-do list for the rest of this week. If you or anyone else is feeling adventurous I would be happy to have the feedback. Cheers! -- Michael R. Crusoe: Software Engineer and Bioinformatician mcrusoe(a)msu.edu @ the Genomics, Evolution, and Development lab; Michigan State University http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670 @biocrusoe

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master_api_key currently doesn't benefit from a real admin's key?!
by Dooley, Damion 21 Nov '14

21 Nov '14

I made the erroneous assumption that if I put my own admin user API key into the galaxy configuration master_api_key field, it would accept that and run all the api functions that needed a key connected to a user. It took fair bit of debugging to realize that the master_api_key field chops off all the user info even if it is available (i.e. has no user object), thus yielding numerous API errors for those things a user object is needed for. I can see a few dev solutions to this dilemma, and am wondering what people think - and the result could get into a Trello feature card... a) allow master_api_key to be accompanied by a master_api_email; together they trigger a user object to be associated that has the email address; and this eliminates all the API errors one currently gets. I like this solution because it doesn't depend on the UI interface for managing user keys, i.e. its rather permanent and secure. b) allow a api key called "admin_api_key" to be placed in the galaxy config file. This key has to be active as one user's api key (presumably power user), so that all those api errors are avoided. c) have master_api_key just have a dummy user object included, with say admin@localhost for an email address. Thoughts? Damion

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Fw: Re: galaxy server file upload problem
by 홍종희 21 Nov '14

21 Nov '14

Thanks for your reply Danon I have tried to setup local galaxy-server in production mode The error that I mentioned occurred when I tried to upload file from my pc to local galaxy server( galaxy server is also installed in same pc ) and my galaxy server is at the root of the domain ( http://127.0.0.1:8080) the attached file is screenshot of error and the other attached file is my nginx configuration file Thanks for your effort in helping me Regards Jonghui ----- Original Message ----- From:Dannon Baker [dannon.baker(a)gmail.com] To:홍종희 [hong(a)syntekabio.com] Cc:Galaxy Dev [galaxy-dev(a)lists.bx.psu.edu] Sent:Wed , November 19, 2014 23:19 PM Subject:Re: [galaxy-dev] galaxy server file upload problem Hi Johngui, Can you specify which request is 404'ing -- the exact URL that's being attempted? And, can you provide a little more of your nginx configuration? Is galaxy being served at the root of the domain? -Dannon On Wed, Nov 19, 2014 at 2:01 AM, 홍종희 < hong(a)syntekabio.com > wrote: Hi galaxy-dev members Recently we're trying to setup the galaxy server in a production mode. Everything seems to be ok but when I tried to upload a file it shows error message like this Failed: Not found(404) I found one thread in galaxy-dev fourn about this one It says that it's because of change in proxy server configuration So I set exactly what was written in Galaxy wiki about nginx configuration related to proxy setting like below set $dst /api/tools; Should I change some oher configuration ? Any kind of suggestion would be welcomed Thanks Regards Jonghui ___________________________________________________________ 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/ div, p { padding: 0px; margin:0cm; margin-bottom:3.5pt; text-align:justify; text-justify:inter-ideograph; text-autospace:none; word-break:break-hangul; font-size: 10pt; }; p.fcknormal, li.fcknormal, div.fcknormal { padding: 0px; margin:0cm; margin-bottom:3.5pt; text-align:justify; text-justify:inter-ideograph; text-autospace:none; word-break:break-hangul; font-size: 10pt };

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Re: [galaxy-dev] galaxy-dev Digest, Vol 101, Issue 29
by Dooley, Damion 20 Nov '14

20 Nov '14

Well, here's one config that should work. I'll guess that you have the same cleanup_datasets/ folder contents as I do so... having logged in as user that galaxy runs under, doing a crontab -e on command line should get you crontab settings for that user. I have an older longer line that handles daily cleanup... 0 0 * * * sh /[path to your galaxy]/galaxy-dist/scripts/cleanup_datasets/delete_userless_histories.sh; sh /usr/local/galaxy/production2/galaxy-dist/scripts/cleanup_datasets/purge_histories.sh; sh /usr/local/galaxy/production2/galaxy-dist/scripts/cleanup_datasets/purge_libraries.sh; sh /usr/local/galaxy/production2/galaxy-dist/scripts/cleanup_datasets/purge_folders.sh; sh /usr/local/galaxy/production2/galaxy-dist/scripts/cleanup_datasets/delete_datasets.sh; sh /usr/local/galaxy/production2/galaxy-dist/scripts/cleanup_datasets/purge_datasets.sh or a more abbreviated version: @daily cd /[path to another galaxy instance]/galaxy-dist/scripts/cleanup_datasets && sh delete_userless_histories.sh && sh purge_histories.sh && sh purge_libraries.sh && sh purge_folders.sh && sh delete_datasets.sh && sh purge_datasets.sh Hopefully that works for you... d. ------------------------------ Message: 4 Date: Wed, 19 Nov 2014 22:14:19 +0000 From: James Mullan <jamespamullan(a)gmail.com> To: galaxy-dev(a)bx.psu.edu Subject: [galaxy-dev] How to get cleanup script to run in cron job ? Message-ID: <CAMk7q9CktOP3QgCSo_8SmtUdD3cbju-H0MNxdFzwPX0g2b4Dww(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello, I am trying to figure out how to run the cleanup scripts in a cron job. The below works on command line:

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Re: [galaxy-dev] galaxy server file upload problem
by 홍종희 20 Nov '14

20 Nov '14

Thanks for your reply Danon I have tried to setup local galaxy-server in production mode The error that I mentioned occurred when I tried to upload file from my pc to local galaxy server( galaxy server is also installed in same pc ) and my galaxy server is at the root of the domain ( http://127.0.0.1:8080) the attached file is screenshot of error and the other attached file is my nginx configuration file Thanks for your effort in helping me Regards Jonghui ----- Original Message ----- From:Dannon Baker [dannon.baker(a)gmail.com] To:홍종희 [hong(a)syntekabio.com] Cc:Galaxy Dev [galaxy-dev(a)lists.bx.psu.edu] Sent:Wed , November 19, 2014 23:19 PM Subject:Re: [galaxy-dev] galaxy server file upload problem Hi Johngui, Can you specify which request is 404'ing -- the exact URL that's being attempted? And, can you provide a little more of your nginx configuration? Is galaxy being served at the root of the domain? -Dannon On Wed, Nov 19, 2014 at 2:01 AM, 홍종희 < hong(a)syntekabio.com > wrote: Hi galaxy-dev members Recently we're trying to setup the galaxy server in a production mode. Everything seems to be ok but when I tried to upload a file it shows error message like this Failed: Not found(404) I found one thread in galaxy-dev fourn about this one It says that it's because of change in proxy server configuration So I set exactly what was written in Galaxy wiki about nginx configuration related to proxy setting like below set $dst /api/tools; Should I change some oher configuration ? Any kind of suggestion would be welcomed Thanks Regards Jonghui ___________________________________________________________ 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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Local Galaxy Apache Config
by Nicholas Kline 19 Nov '14

19 Nov '14

Hello Galaxy Admins, I am attempting to setup a local production-grade Galaxy server for our department. Before I go ahead and "turn on" Galaxy for the first time, would you be so kind as to please review my Apache2 config files for errors? I want to be sure that things are in the correct place to save me from headaches down the road. The overall goals of the configuration are: - always use HTTPS and secure FTP - make maximum use of the machine (multiple Apache processes, PostgreSQL, ProFTPD, etc.) If it helps, Galaxy will be running on a: - Dell Precision T7500 - 2 x Intel Xeon X5690 @ 3.46 GHz - 96 GB RAM - Ubuntu 14.04 64-bit Thank you for your help! FYI: My config files are based on the instructions at https://wiki.galaxyproject.org/Admin/GetGalaxy and https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer ############################## # # /etc/apache2/apache2.conf # ############################## # Global configuration # # ServerRoot: The top of the directory tree under which the server's # configuration, error, and log files are kept. # # NOTE! If you intend to place this on an NFS (or otherwise network) # mounted filesystem then please read the Mutex documentation (available # at <URL:http://httpd.apache.org/docs/2.4/mod/core.html#mutex>); # you will save yourself a lot of trouble. # # Do NOT add a slash at the end of the directory path. # #ServerRoot "/etc/apache2" # # The accept serialization lock file MUST BE STORED ON A LOCAL DISK. # Mutex file:${APACHE_LOCK_DIR} default # # PidFile: The file in which the server should record its process # identification number when it starts. # This needs to be set in /etc/apache2/envvars # PidFile ${APACHE_PID_FILE} # # Timeout: The number of seconds before receives and sends time out. # Timeout 300 # # KeepAlive: Whether or not to allow persistent connections (more than # one request per connection). Set to "Off" to deactivate. # KeepAlive On # # MaxKeepAliveRequests: The maximum number of requests to allow # during a persistent connection. Set to 0 to allow an unlimited amount. # We recommend you leave this number high, for maximum performance. # MaxKeepAliveRequests 100 # # KeepAliveTimeout: Number of seconds to wait for the next request from the # same client on the same connection. # KeepAliveTimeout 5 # These need to be set in /etc/apache2/envvars User ${APACHE_RUN_USER} Group ${APACHE_RUN_GROUP} # # HostnameLookups: Log the names of clients or just their IP addresses # e.g., www.apache.org (on) or 204.62.129.132 (off). # The default is off because it'd be overall better for the net if people # had to knowingly turn this feature on, since enabling it means that # each client request will result in AT LEAST one lookup request to the # nameserver. # HostnameLookups Off # ErrorLog: The location of the error log file. # If you do not specify an ErrorLog directive within a <VirtualHost> # container, error messages relating to that virtual host will be # logged here. If you *do* define an error logfile for a <VirtualHost> # container, that host's errors will be logged there and not here. # ErrorLog ${APACHE_LOG_DIR}/error.log # # LogLevel: Control the severity of messages logged to the error_log. # Available values: trace8, ..., trace1, debug, info, notice, warn, # error, crit, alert, emerg. # It is also possible to configure the log level for particular modules, e.g. # "LogLevel info ssl:warn" # LogLevel warn # Include module configuration: IncludeOptional mods-enabled/*.load IncludeOptional mods-enabled/*.conf # Include list of ports to listen on Include ports.conf # Sets the default security model of the Apache2 HTTPD server. It does # not allow access to the root filesystem outside of /usr/share and /var/www. # The former is used by web applications packaged in Debian, # the latter may be used for local directories served by the web server. If # your system is serving content from a sub-directory in /srv you must allow # access here, or in any related virtual host. <Directory /> Options FollowSymLinks AllowOverride None Require all denied </Directory> <Directory /usr/share> AllowOverride None Require all granted </Directory> <Directory /var/www/> Options Indexes FollowSymLinks AllowOverride None Require all granted </Directory> #<Directory /srv/> # Options Indexes FollowSymLinks # AllowOverride None # Require all granted #</Directory> # AccessFileName: The name of the file to look for in each directory # for additional configuration directives. See also the AllowOverride # directive. # AccessFileName .htaccess # # The following lines prevent .htaccess and .htpasswd files from being # viewed by Web clients. # <FilesMatch "^\.ht"> Require all denied </FilesMatch> # # The following directives define some format nicknames for use with # a CustomLog directive. # # These deviate from the Common Log Format definitions in that they use %O # (the actual bytes sent including headers) instead of %b (the size of the # requested file), because the latter makes it impossible to detect partial # requests. # # Note that the use of %{X-Forwarded-For}i instead of %h is not recommended. # Use mod_remoteip instead. # LogFormat "%v:%p %h %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"" vhost_combined LogFormat "%h %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"" combined LogFormat "%h %l %u %t \"%r\" %>s %O" common LogFormat "%{Referer}i -> %U" referer LogFormat "%{User-agent}i" agent # Include of directories ignores editors' and dpkg's backup files, # see README.Debian for details. <Location "/"> # Makes galaxy aware of what type of URL it should generate for external sites like Biomart. RequestHeader set X-URL-SCHEME https # Compress all uncompressed content. SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary # This speeds up downloads. XSendFile on XSendFilePath / </Location> <Location "/static"> # Allow browsers to cache everything from /static for 6 hours ExpiresActive On ExpiresDefault "access plus 6 hours" </Location> # Include generic snippets of statements IncludeOptional conf-enabled/*.conf # Include the virtual host configurations: IncludeOptional sites-enabled/*.conf # vim: syntax=apache ts=4 sw=4 sts=4 sr noet ############################## # # /etc/apache2/sites-available/000-default.conf # ############################## <VirtualHost *:80> # The ServerName directive sets the request scheme, hostname and port that # the server uses to identify itself. This is used when creating # redirection URLs. In the context of virtual hosts, the ServerName # specifies what hostname must appear in the request's Host: header to # match this virtual host. For the default virtual host (this file) this # value is not decisive as it is used as a last resort host regardless. # However, you must set it for any further virtual host explicitly. ServerName computer.school.edu ServerAdmin awesome.admin(a)school.edu DocumentRoot /var/www/html # Available loglevels: trace8, ..., trace1, debug, info, notice, warn, # error, crit, alert, emerg. # It is also possible to configure the loglevel for particular # modules, e.g. #LogLevel info ssl:warn ErrorLog ${APACHE_LOG_DIR}/error.log CustomLog ${APACHE_LOG_DIR}/access.log combined # For most configuration files from conf-available/, which are # enabled or disabled at a global level, it is possible to # include a line for only one particular virtual host. For example the # following line enables the CGI configuration for this host only # after it has been globally disabled with "a2disconf". #Include conf-available/serve-cgi-bin.conf # Allow display sites such as UCSC. <Location "/root/display_as"> Satisfy Any Order deny,allow Deny from all Allow from hgw1.cse.ucsc.edu Allow from hgw2.cse.ucsc.edu Allow from hgw3.cse.ucsc.edu Allow from hgw4.cse.ucsc.edu Allow from hgw5.cse.ucsc.edu Allow from hgw6.cse.ucsc.edu Allow from hgw7.cse.ucsc.edu Allow from hgw8.cse.ucsc.edu </Location> #<Proxy balancer://galaxy> # BalancerMember http://localhost:8400 # BalancerMember http://localhost:8401 #</Proxy> <Proxy balancer://galaxy> BalancerMember http://localhost:8080 BalancerMember http://localhost:8081 BalancerMember http://localhost:8082 BalancerMember http://localhost:8083 BalancerMember http://localhost:8084 BalancerMember http://localhost:8085 BalancerMember http://localhost:8086 BalancerMember http://localhost:8087 BalancerMember http://localhost:8088 BalancerMember http://localhost:8089 </Proxy> # Proxy requests to the Galaxy application. RewriteEngine on RewriteRule ^/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] # This line: #RewriteRule ^(.*) http://localhost:8080$1 [P] # ...replaced with this line: RewriteRule ^(.*) balancer://galaxy$1 [P] </VirtualHost> # vim: syntax=apache ts=4 sw=4 sts=4 sr noet ############################## # # /etc/apache2/sites-available/default-ssl.conf # ############################## <IfModule mod_ssl.c> <VirtualHost _default_:443> ServerAdmin awesome.admin(a)school.edu DocumentRoot /var/www/html # Available loglevels: trace8, ..., trace1, debug, info, notice, warn, # error, crit, alert, emerg. # It is also possible to configure the loglevel for particular # modules, e.g. #LogLevel info ssl:warn ErrorLog ${APACHE_LOG_DIR}/error.log CustomLog ${APACHE_LOG_DIR}/access.log combined # For most configuration files from conf-available/, which are # enabled or disabled at a global level, it is possible to # include a line for only one particular virtual host. For example the # following line enables the CGI configuration for this host only # after it has been globally disabled with "a2disconf". #Include conf-available/serve-cgi-bin.conf # SSL Engine Switch: # Enable/Disable SSL for this virtual host. SSLEngine on # A self-signed (snakeoil) certificate can be created by installing # the ssl-cert package. See # /usr/share/doc/apache2/README.Debian.gz for more info. # If both key and certificate are stored in the same file, only the # SSLCertificateFile directive is needed. #SSLCertificateFile /etc/ssl/certs/ssl-cert-snakeoil.pem #SSLCertificateKeyFile /etc/ssl/private/ssl-cert-snakeoil.key SSLCertificateFile /etc/ssl/certs/server.crt SSLCertificateKeyFile /etc/ssl/private/server.key # Server Certificate Chain: # Point SSLCertificateChainFile at a file containing the # concatenation of PEM encoded CA certificates which form the # certificate chain for the server certificate. Alternatively # the referenced file can be the same as SSLCertificateFile # when the CA certificates are directly appended to the server # certificate for convinience. #SSLCertificateChainFile /etc/apache2/ssl.crt/server-ca.crt # Certificate Authority (CA): # Set the CA certificate verification path where to find CA # certificates for client authentication or alternatively one # huge file containing all of them (file must be PEM encoded) # Note: Inside SSLCACertificatePath you need hash symlinks # to point to the certificate files. Use the provided # Makefile to update the hash symlinks after changes. #SSLCACertificatePath /etc/ssl/certs/ #SSLCACertificateFile /etc/apache2/ssl.crt/ca-bundle.crt # Certificate Revocation Lists (CRL): # Set the CA revocation path where to find CA CRLs for client # authentication or alternatively one huge file containing all # of them (file must be PEM encoded) # Note: Inside SSLCARevocationPath you need hash symlinks # to point to the certificate files. Use the provided # Makefile to update the hash symlinks after changes. #SSLCARevocationPath /etc/apache2/ssl.crl/ #SSLCARevocationFile /etc/apache2/ssl.crl/ca-bundle.crl # Client Authentication (Type): # Client certificate verification type and depth. Types are # none, optional, require and optional_no_ca. Depth is a # number which specifies how deeply to verify the certificate # issuer chain before deciding the certificate is not valid. #SSLVerifyClient require #SSLVerifyDepth 10 # SSL Engine Options: # Set various options for the SSL engine. # o FakeBasicAuth: # Translate the client X.509 into a Basic Authorisation. This means that # the standard Auth/DBMAuth methods can be used for access control. The # user name is the `one line' version of the client's X.509 certificate. # Note that no password is obtained from the user. Every entry in the user # file needs this password: `xxj31ZMTZzkVA'. # o ExportCertData: # This exports two additional environment variables: SSL_CLIENT_CERT and # SSL_SERVER_CERT. These contain the PEM-encoded certificates of the # server (always existing) and the client (only existing when client # authentication is used). This can be used to import the certificates # into CGI scripts. # o StdEnvVars: # This exports the standard SSL/TLS related `SSL_*' environment variables. # Per default this exportation is switched off for performance reasons, # because the extraction step is an expensive operation and is usually # useless for serving static content. So one usually enables the # exportation for CGI and SSI requests only. # o OptRenegotiate: # This enables optimized SSL connection renegotiation handling when SSL # directives are used in per-directory context. #SSLOptions +FakeBasicAuth +ExportCertData +StrictRequire <FilesMatch "\.(cgi|shtml|phtml|php)$"> SSLOptions +StdEnvVars </FilesMatch> <Directory /usr/lib/cgi-bin> SSLOptions +StdEnvVars </Directory> # SSL Protocol Adjustments: # The safe and default but still SSL/TLS standard compliant shutdown # approach is that mod_ssl sends the close notify alert but doesn't wait for # the close notify alert from client. When you need a different shutdown # approach you can use one of the following variables: # o ssl-unclean-shutdown: # This forces an unclean shutdown when the connection is closed, i.e. no # SSL close notify alert is send or allowed to received. This violates # the SSL/TLS standard but is needed for some brain-dead browsers. Use # this when you receive I/O errors because of the standard approach where # mod_ssl sends the close notify alert. # o ssl-accurate-shutdown: # This forces an accurate shutdown when the connection is closed, i.e. a # SSL close notify alert is send and mod_ssl waits for the close notify # alert of the client. This is 100% SSL/TLS standard compliant, but in # practice often causes hanging connections with brain-dead browsers. Use # this only for browsers where you know that their SSL implementation # works correctly. # Notice: Most problems of broken clients are also related to the HTTP # keep-alive facility, so you usually additionally want to disable # keep-alive for those clients, too. Use variable "nokeepalive" for this. # Similarly, one has to force some clients to use HTTP/1.0 to workaround # their broken HTTP/1.1 implementation. Use variables "downgrade-1.0" and # "force-response-1.0" for this. BrowserMatch "MSIE [2-6]" \ nokeepalive ssl-unclean-shutdown \ downgrade-1.0 force-response-1.0 # MSIE 7 and newer should be able to use keepalive BrowserMatch "MSIE [17-9]" ssl-unclean-shutdown </VirtualHost> </IfModule> # vim: syntax=apache ts=4 sw=4 sts=4 sr noet

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Problem to upload data to Galaxy when using pbed file format
by tjkarlsson＠uma.es 19 Nov '14

19 Nov '14

Dear all, I am trying to upload data from PLINK (.bed, .bim and .fam-files) for the pbed file format using a local installation of Galaxy but it is not working. The local Galaxy installation was done yesterday, following the instructions at: https://wiki.galaxyproject.org/Admin/GetGalaxy First, I click on the Get Data tool, I then select pbed as "File Format", the page reloads and I now can enter the three files (.bed, .bim, .fam). Once I click "Execute" the job starts but never seems to finish. If I look in the log output from Galaxy I get the following error: galaxy.tools ERROR 2014-11-13 13:24:52,226 Exception caught while attempting tool execution: Traceback (most recent call last): File "/home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 2180, in handle_single_execution job, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id ) File "/home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 2738, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/actions/upload.py", line 21, in execute uploaded_datasets = upload_common.get_uploaded_datasets( trans, '', incoming, precreated_datasets, dataset_upload_inputs, history=history ) File "/home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/actions/upload_common.py", line 246, in get_uploaded_datasets data.uuid = uploaded_dataset.uuid AttributeError: 'Bunch' object has no attribute 'uuid' Any idea what could be the problem? Kind regards, Johan

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Public toolshed giving "internal server error"
by Peter Briggs 19 Nov '14

19 Nov '14

Hello I'm trying to make a new repository on the public toolshed at https://toolshed.g2.bx.psu.edu/ but I keep getting the "internal server error" page. I was also unable to log out, or even to see the front page when trying to access it from a different browser. Is anyone else having this problem? Thanks & best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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galaxy server file upload problem
by 홍종희 19 Nov '14

19 Nov '14

Hi galaxy-dev members Recently we're trying to setup the galaxy server in a production mode. Everything seems to be ok but when I tried to upload a file it shows error message like this Failed: Not found(404) I found one thread in galaxy-dev fourn about this one It says that it's because of change in proxy server configuration So I set exactly what was written in Galaxy wiki about nginx configuration related to proxy setting like below set $dst /api/tools; Should I change some oher configuration ? Any kind of suggestion would be welcomed Thanks Regards Jonghui

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how to use api to log in Galaxy?
by xlwang 19 Nov '14

19 Nov '14

Hi, I want to integrate Galaxy with another system. When I log in this system, then click a link jump to Galaxy, this user has already logged into Galaxy. Now, I can use api to create a user at the same time in this system and Galaxy, but how to use api to log in Galaxy?

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