Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails
Dear all, I am having the same problem as Linda with a fresh installation of version 20130603. In the thread of her mail Dannon Baker said : That said, this doesn't resolve the mysql index issues, which I'm currently working on. I hope to have a fix for them available soon, though. I would like to know if what is the status of this thread. Should I use the solution provided in Linda's mail (CREATE INDEX ix_history_slug ON history (slug(1000));) Thx a lot for your help Best Jean-François On 06/05/2013 05:12 PM, Linda Cham wrote: Hi. I am new to the Galaxy forum and I am trying to setup a new local Galaxy instance with MySQL on RH6.2 x86_64. On a newly installed OS node, using the hg clone command (hg clone _https://bitbucket.org/galaxy/galaxy-dist#stable_ https://bitbucket.org/galaxy/galaxy-dist) which gets the current Galaxy 20130603 image, I am getting the following errors when running run.sh: File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173, in execute self.errorhandler(self, exc, value) File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36, in defaulterrorhandler raise errorclass, errorvalue OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' used in key specification without a key length) 'CREATE INDEX ix_history_slug ON history (slug)' () Reading the forum, someone stated it can be bypass by running the CREATE INDEX. mysql CREATE INDEX ix_history_slug ON history (slug(1000)); Query OK, 0 rows affected (0.09 sec) Records: 0 Duplicates: 0 Warnings: 0 -- # Jean-François Taly Bioinformatician Bioinformatics Core Facility http://biocore.crg.cat CRG - Centre de Regulació Genòmica (Room 439) Parc de Recerca Biomèdica de Barcelona (PRBB) Doctor Aiguader, 88 08003 Barcelona Spain email: jean-francois.t...@crg.eu phone: +34 93 316 0202 fax: +34 93 316 0099 # ___ 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] Installation of 20130603 Galaxy image with MySQL fails
Hi Jean-François, The index issues preventing a new instance from starting are resolved in the stable branch of galaxy-central; if you pull updates from that branch you should be able to start a new instance. While the instance will start and run, there are other peculiarities I still need to resolve and I'd really recommend using postgres for a new instance at this time if you're at all able to do so. -Dannon On Fri, Jun 21, 2013 at 5:07 AM, jean-François Taly jean-francois.t...@crg.eu wrote: Dear all, I am having the same problem as Linda with a fresh installation of version 20130603. In the thread of her mail Dannon Baker said : That said, this doesn't resolve the mysql index issues, which I'm currently working on. I hope to have a fix for them available soon, though. I would like to know if what is the status of this thread. Should I use the solution provided in Linda's mail (CREATE INDEX ix_history_slug ON history (slug(1000));) Thx a lot for your help Best Jean-François On 06/05/2013 05:12 PM, Linda Cham wrote: Hi. I am new to the Galaxy forum and I am trying to setup a new local Galaxy instance with MySQL on RH6.2 x86_64. On a newly installed OS node, using the hg clone command (hg clone * https://bitbucket.org/galaxy/galaxy-dist#stable*https://bitbucket.org/galaxy/galaxy-dist) which gets the current Galaxy 20130603 image, I am getting the following errors when running run.sh: File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173, in execute self.errorhandler(self, exc, value) File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36, in defaulterrorhandler raise errorclass, errorvalue OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' used in key specification without a key length) 'CREATE INDEX ix_history_slug ON history (slug)' () Reading the forum, someone stated it can be bypass by running the CREATE INDEX. mysql CREATE INDEX ix_history_slug ON history (slug(1000)); Query OK, 0 rows affected (0.09 sec) Records: 0 Duplicates: 0 Warnings: 0 -- # Jean-François Taly Bioinformatician Bioinformatics Core Facilityhttp://biocore.crg.cat CRG - Centre de Regulació Genòmica (Room 439) Parc de Recerca Biomèdica de Barcelona (PRBB) Doctor Aiguader, 88 08003 Barcelona Spain email: jean-francois.t...@crg.eu phone: +34 93 316 0202 fax: +34 93 316 0099 # ___ 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/
Re: [galaxy-dev] visulaization tool
Hi James, galaxy.pdb is a dataset in galaxy , which is shown by this url http://10.180.8.54:9098/display_application/1fad1eaf5f4f1766/jmol_pdb/jmol_main/5da8464cb811e1a6/data/galaxy.pdb. i want to download this link in galaxy by using python or java . after downloading,downloaded file contains only html tags ..not the actual content . it wont's display the actual contents. Regards shashi From: James Taylor ja...@taylorlab.org To: shashi shekhar me_shash...@yahoo.co.in Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Sent: Thursday, 20 June 2013 8:57 PM Subject: Re: [galaxy-dev] visulaization tool Display applications are extensively documented here: http://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Applications%20Tutorial -- James Taylor, Assistant Professor, Biology/CS, Emory University On Thu, Jun 20, 2013 at 2:20 AM, shashi shekhar me_shash...@yahoo.co.in wrote: Hi james, can you share some examples of display application . and in which tool you use for display application in galaxy ? Regards shashi From: James Taylor ja...@taylorlab.org To: shashi shekhar me_shash...@yahoo.co.in Cc: Ross ross.laza...@gmail.com; galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Sent: Wednesday, 19 June 2013 7:03 PM Subject: Re: [galaxy-dev] visulaization tool Tightly integrated interactive visualizations like Trackster need to be web based (implemented in Javascript). See our paper that just came out in BMC genomics. Note there is already a phylogenetic tree visualization tool (phyloviz) that was built by Tomithy Too. Extensions to that for additional features would be welcome. For a Java based visualization tool you need to take a completely different approach. Look at Display Applications support, specifically examples like IGB and IGV. On Jun 19, 2013, at 7:56 AM, shashi shekhar me_shash...@yahoo.co.in wrote: Hi Ross, Actually i have to add the visualization which will be interactive . it will take dataset from galaxy .it will be in the same way as tracker works . in stead of tracker i want to add my own visualization tool. from wehere should i start to replace tracker with my own visulization tool. Regards shashi From: Ross ross.laza...@gmail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Hans-Rudolf Hotz h...@fmi.ch; galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Sent: Wednesday, 19 June 2013 5:02 PM Subject: Re: [galaxy-dev] visulaization tool Shashi, Thanks for the additional information. AFAIK: If it's command line driven and spews out pdf's, adapt any similar tool that spews out pdfs like fastqc. Galaxy tool execution is isolated from the user and from Galaxy itself, so communication is just not possible if it's interactive - unless you hack the tool into Galaxy itself or something. There is no documentation for that. On Wed, Jun 19, 2013 at 9:01 PM, shashi shekhar me_shash...@yahoo.co.in wrote: Hi Ross, thanks for the reply . actually i want to use TreeView as visulaization tool. TreeView X is an open source and multi-platform program to display phylogenetic trees. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It allows one to order the branches of the trees, and to export the trees in SVG format. i have to add treeviewx in galaxy.. Regards shashi From: Ross ross.laza...@gmail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Hans-Rudolf Hotz h...@fmi.ch; galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Sent: Wednesday, 19 June 2013 3:28 PM Subject: Re: [galaxy-dev] visulaization tool Shashi, Hans made a brave guess based on your vague question, but you'll probably get better answers if you do us all a favour and make an effort to provide unambiguous detail about exactly what you want to achieve. If there is a working Galaxy tool that does what you need but using a different visualisation program (whatever you mean by that vague term), substituting your executable will probably be relatively trivial. eg do you consider the Html object produced by the fastqc or the image from the scatterplot tool to be visualisation program outputs? If so, clone a working tool. On Wed, Jun 19, 2013 at 5:37 PM, shashi shekhar me_shash...@yahoo.co.in wrote: Hi, I want to add the the complete separate tool in galaxy . how will i do it ..i don't want to use existing visulaization tool. Regards shashi From: Hans-Rudolf Hotz h...@fmi.ch To: shashi shekhar me_shash...@yahoo.co.in Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Sent: Wednesday, 19 June 2013 12:29 PM Subject: Re: [galaxy-dev] visulaization tool Hi Shashi Have a look at:
Re: [galaxy-dev] nglims roles
Lee; Glad the capitalization role change got things working smoothly for permissions. I guess one more question for today. Our lab will be taking care of all library preps and so we want to simplify and remove a few options including Multiplexing/barcodes, library construction, and library validation. Where would I change that in nglims? I can't seem to hack it in the yaml file. There is some rudimentary support for modifying this by changing the YAML configuration in tool-data/nglims.yaml. After you edit the file you need to re-update the database with the new form definitions using: python scripts/nglims/add_ng_defaults.py universe_wsgi.ini It's a little hacky in terms of configuration, but hopefully that will get you what you need. Thanks much, Brad Thanks for your help. On Thu, Jun 20, 2013 at 4:35 PM, Lee Katz lsk...@gmail.com wrote: After a lot of head banging and then realizing that you stressed sequencing I realized I had a capitalization error. Case-sensitive! Everything seems to be working fine now, and I will be customizing it some more via the yaml file. Thank you Brad. You are awesome that you are so responsive. On Thu, Jun 20, 2013 at 9:35 AM, Brad Chapman chapm...@50mail.com wrote: Lee; Hi, what roles are embedded in nglims? (am I calling it by the right name?) I have a sequencing role which will be given to anyone submitting a request, and that seems to be working just fine. I am also using the yaml form to edit the submission form, and I think it's beautifully implemented. The sequencing role is the only embedded role and is for the sequencing team, not individual researchers submitting samples. Individuals researchers can be regular Galaxy users and will have access to all of the sample submission forms but not the web forms to move samples through the back end process. The idea with the sequencing role was exactly as you describe. Give the sequencing team access to nglims sample tracking without needing them to be administrators on Galaxy. Glad you've got things up and running, Brad -- Lee Katz, Ph.D. -- Lee Katz, Ph.D. ___ 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] Installation of 20130603 Galaxy image with MySQL fails
Thanks Dannon, I indeed managed to have the galaxy-central version installed. I already see some problems but I will open another thread if necessary. Regards the DB engine, this new Galaxy I am deploying now is only a toy server I want to use in the Galaxy meeting in Oslo. I would like to have the same configuration as the other server we already have which using MySQL. Thx a lot for your help JF On 06/21/2013 11:26 AM, Dannon Baker wrote: Hi Jean-François, The index issues preventing a new instance from starting are resolved in the stable branch of galaxy-central; if you pull updates from that branch you should be able to start a new instance. While the instance will start and run, there are other peculiarities I still need to resolve and I'd really recommend using postgres for a new instance at this time if you're at all able to do so. -Dannon On Fri, Jun 21, 2013 at 5:07 AM, jean-François Taly jean-francois.t...@crg.eu mailto:jean-francois.t...@crg.eu wrote: Dear all, I am having the same problem as Linda with a fresh installation of version 20130603. In the thread of her mail Dannon Baker said : That said, this doesn't resolve the mysql index issues, which I'm currently working on. I hope to have a fix for them available soon, though. I would like to know if what is the status of this thread. Should I use the solution provided in Linda's mail (CREATE INDEX ix_history_slug ON history (slug(1000));) Thx a lot for your help Best Jean-François On 06/05/2013 05:12 PM, Linda Cham wrote: Hi. I am new to the Galaxy forum and I am trying to setup a new local Galaxy instance with MySQL on RH6.2 x86_64. On a newly installed OS node, using the hg clone command (hg clone _https://bitbucket.org/galaxy/galaxy-dist#stable_ https://bitbucket.org/galaxy/galaxy-dist) which gets the current Galaxy 20130603 image, I am getting the following errors when running run.sh: File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173, in execute self.errorhandler(self, exc, value) File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36, in defaulterrorhandler raise errorclass, errorvalue OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' used in key specification without a key length) 'CREATE INDEX ix_history_slug ON history (slug)' () Reading the forum, someone stated it can be bypass by running the CREATE INDEX. mysql CREATE INDEX ix_history_slug ON history (slug(1000)); Query OK, 0 rows affected (0.09 sec) Records: 0 Duplicates: 0 Warnings: 0 -- # Jean-François Taly Bioinformatician Bioinformatics Core Facility http://biocore.crg.cat CRG - Centre de Regulació Genòmica (Room 439) Parc de Recerca Biomèdica de Barcelona (PRBB) Doctor Aiguader, 88 08003 Barcelona Spain email:jean-francois.t...@crg.eu mailto:jean-francois.t...@crg.eu phone:+34 93 316 0202 tel:%2B34%2093%20316%200202 fax:+34 93 316 0099 tel:%2B34%2093%20316%200099 # ___ 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/ -- # Jean-François Taly Bioinformatician Bioinformatics Core Facility http://biocore.crg.cat CRG - Centre de Regulació Genòmica (Room 439) Parc de Recerca Biomèdica de Barcelona (PRBB) Doctor Aiguader, 88 08003 Barcelona Spain email:jean-francois.t...@crg.eu phone: +34 93 316 0202 fax: +34 93 316 0099 # ___ 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] Tophat2 output issue on LWR runner
Hi John Thank you for the reply. In the lwr_staging directory all the runs from tophat are kept in (separate folders for each run) which means that the job failed to finish. In the paster.log the most common error is HTTPNotFound: No file found with path lwr_staging/uniquejobstring/working/insertions.bed That's the case when tophat's output is set at default and the outputs are under working/tophat_out/. If I change this in the wrapper and redirect the output in working/ I get the following error. Traceback (most recent call last): File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr.py, line 135, in finish_job client.download_work_dir_output(source_file, job_wrapper.working_directory, output_file) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 146, in download_work_dir_output self.__raw_download_output(name, self.job_id, work_dir, output) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 174, in __raw_download_output output_path=output_path) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 52, in __raw_execute response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py, line 26, in execute with open(output_path, 'wb') as output: TypeError: coercing to Unicode: need string or buffer, file found or one time I got this Groomed 75 sanger reads into sanger reads. Based upon quality and sequence, the input data is valid for: solexa, sanger, illumina Input ASCII range: 'B'(66) - 'b'(98) Input decimal range: 33 - 65 In the last two cases, no error was logged in lwr/paster.log Bests, Nikos 2013/6/18 John Chilton chil...@msi.umn.edu Hey Nikos, Thanks for the interest in the LWR and frankly I am excited to hear that bowtie worked properly. Some of these core NGS tools that require implicit indices spanning multiple files are not really addressed by the LWR currently, it only knows how to stage files that actually appear in the command-line or a config file. I guess if you are just using files from the history this is not a problem, but it is something to be aware of if you plan to start using .loc files. My first thought is that the LWR might not support 'from_work_dir' outputs in nested subdirectories. I will have to look more closely at that. Something that will help me though, is knowing if TopHat produced the outputs. Can you look at the LWR staging directory and tell me if these files were created (by default when a job fails, it is not cleaned up this is configurable in galaxy-central but not in galaxy-dist right now)? Also, does the LWR have any useful logs available? These will likely be in paster.log in the LWR directory. Also, the tip of galaxy-central includes improved error logging and exception handling so it is possible it would produce a better error message than this admittedly cryptic problem. I know it is not always possible to upgrade, but if it is easy it is something worth considering doing. -John On Tue, Jun 18, 2013 at 8:18 AM, Nikos Sidiropoulos nikos.sid...@gmail.com wrote: Hi We are running the latest stable distribution on our server. We want tophat2 (along with other tools) to be executed on another machine. LWR is setup based on the online documentation (http://wiki.galaxyproject.org/Admin/Config/LWR, https://lwr.readthedocs.org/en/latest/) Bowtie2 is working as should but it looks like LWR is unable to return the outputs from tophat2. In universe_wsgi.ini the runner is configured like this: [galaxy:tool_runners] bowtie2 = lwr://https://uniquestring@chaos:8913 tophat2 = lwr://https://uniquestring@chaos:8913 When running tophat2 the following error message is returned. Traceback (most recent call last): File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr.py, line 135, in finish_job client.download_work_dir_output(source_file, job_wrapper.working_directory, output_file) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 146, in download_work_dir_output self.__raw_download_output(name, self.job_id, work_dir, output) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 174, in __raw_download_output output_path=output_path) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py, line 52, in __raw_execute response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py, line 21, in execute response = self._url_open(request, data) File /hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py, line 12, in
Re: [galaxy-dev] Portable tool identifiers in workflows
On Fri, Jun 14, 2013 at 1:40 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, On Jun 13, 2013, at 4:14 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Jun 13, 2013 at 6:34 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Peter, Unfortunately, workflows are currently not very compatible with the tool shed - there is a Trello card that details the issues here: https://trello.com/card/workflow-issues/506338ce32ae458f6d15e4b3/692 Thanks Greg - I see that Trello card is in progress, but it covers quite a broad range of issues. These long standing issues are the reason I am not marketing workflow use in the tool shed in a more prominent way. You may have noticed that importing workflows from an installed tool shed repository into Galaxy is not a simple process. I have not worked on streamlining this process (or other workflow related features for the tool shed) due to these same issues. cut For anyone else interested, some good news from Dannon: On Fri, Jun 21, 2013 at 10:27 AM, Dannon Baker wrote: All those issues in the trello card should be resolved now, importing workflows should work as expected. -Dannon Excellent news - thank you all :) Peter ___ 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] Styling the Galaxy tool config xml
Hi, I'm trying to see if I can style Galaxy tools, so instead of all the input fields being a long list one after the other, I can align a few of the fields side-by-side. Has anyone any suggestions on how I might accomplish this? Best wishes, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 ___ 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] ProFTPD integration with Galaxy
Ricardo, I followed the advice you offered back-channel and backed off the galaxy changes to support pbkdf2. I can now authenticate via the latest stable release of ProFTPD. Thanks! Malcolm On Thursday 20 June 2013 10:54:44 Perez, Ricardo wrote: I am sorry, i posted the wrong configuration file above. I am posting now the updated proftpd.conf , the differences is that some things are commented out and others are not. # This is a basic ProFTPD configuration file (rename it to # 'proftpd.conf' for actual use. It establishes a single server # and a single anonymous login. It assumes that you have a user/group # nobody and ftp for normal operation and anon. ServerNameGenomics01 ProFTPd ServerTypestandalone DefaultServer on DeferWelcomeoff UseIPv6 on IdentLookupsoff MultilineRFC2228on ShowSymlinkson ModulePath /usr/local/galaxy/downloads/proftpd-1.3.5rc3/modules/ LoadModulemod_sql.c LoadModulemod_sql_postgres.c LoadModulemod_sql_passwd.c IfModule mod_sql.c SQLBackendpostgres SQLEngine on SQLAuthenticate users SQLAuthTypes SHA1 SHA256 pbkdf2 SQLPasswordPBKDF2 SHA256 1000 24 #SQLPasswordSaltFile /path/to/file SQLConnectInfogalaxydb@localhost:5432 ftpuser mypassword SQLUserInfo custom:/LookupGalaxyUser #SQLNamedQueryLookupGalaxyUser SELECT email,password,'galaxy','galaxy','/usr/local/galaxy/galaxy-dist/database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U' SQLPasswordUserSalt sql:/GetUserSalt SQLNamedQuery LookupGalaxyUser SELECT email, (CASE WHEN substring(password from 1 for 6) = 'PBDKF2' THEN substring(password from 38 for 69) ELSE password END) AS password2,'galaxy','galaxy','/usr/local/galaxy/galaxy-dist/database/ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U' SQLNamedQuery GetUserSalt SELECT (CASE WHEN SUBSTRING (password from 1 for 6) = 'PBDKF2' THEN SUBSTRING (password from 21 for 36) END) AS salt FROM galaxy_user WHERE email='%U' /IfModule SQLDefaultGID 1002 SQLDefaultUID 1002 TimeoutNoTransfer 600 TimeoutStalled 600 TimeoutIdle 1200 DisplayLoginwelcome.msg DisplayChdir.message true ListOptions -l DenyFilter \*.*/ # Use this to jail all users in their homes DefaultRoot ~ CreateHome on dirmode 700 AllowOverwrite on AllowStoreRestart on SQLPasswordEngine on SQLPasswordEncoding hex PassivePorts 3 4 # Port 21 is the standard FTP port. Port 21 # Don't use IPv6 support by default. # Umask 022 is a good standard umask to prevent new dirs and files # from being group and world writable. Umask 077 # To prevent DoS attacks, set the maximum number of child processes # to 30. If you need to allow more than 30 concurrent connections # at once, simply increase this value. Note that this ONLY works # in standalone mode, in inetd mode you should use an inetd server # that allows you to limit maximum number of processes per service # (such as xinetd). MaxInstances 30 # Set the user and group under which the server will run. User galaxy Group galaxy # To cause every FTP user to be jailed (chrooted) into their home # directory, uncomment this line. #DefaultRoot ~ # Normally, we want files to be overwriteable. AllowOverwriteon AuthOrder mod_sql.c # Bar use of SITE CHMOD by default #Limit SITE_CHMOD # DenyAll #/Limit Include /etc/proftpd/conf.d/ ___ 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/ -- Malcolm Tobias 314.362.1594 ___ 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:
