Re: [galaxy-dev] New Tool Shed: Inconsistent field names
On Tue, Jul 5, 2011 at 7:24 PM, Greg Von Kuster g...@bx.psu.edu wrote: I have previously commented on the problem with showing the description on its own without the context of the tool name as displayed in Galaxy: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-June/005640.html and: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004012.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004017.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004019.html One idea would be to show just the name in the left hand pane of Galaxy, with the description as a tool tip AND show this at the top of the tool main page in the central panel. This would encourage tool authors to write this field as a self contained synopsis, and make the left hand panel less text heavy. This may be considered for the Galaxy instance (the decision is in the hands of others), but would probably not work in the tool shed. Again, we'll see what we can improve as I make progress on the repository metadata implementation. Sorry if that was unclear, I did mean the main Galaxy interface there. 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/
Re: [galaxy-dev] Cleanup scripts - question or bug ?
Hello Assaf, Thanks very much for your patch - I've applied it in change set 5770:a5e0a5d3c0a1. Greg Von Kuster On Jul 1, 2011, at 5:35 PM, Assaf Gordon wrote: Hi, I'm trying to use the built-in cleanup scripts (instead of my own), came across a possible bug: 1. When running delete_datasets.sh, the info_only flag is ignored. This is evident by running it twice with -i and getting different results (the second time - no datasets are deleted). 2. When running purge_datasets.sh with the info_only flag, no information is printed at all, making it impossible to know what would be purged without the -i flag. The only way to see what is purged is actually purging the datasets (kind of defeats the purpose of info only). I think the attached patch fixes both issues. 3. The relevant wiki page (https://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDatasets) says about delete_datasets.sh: The purge_datasets.sh script will need to be run afterwards to remove the base datasets from disk. But the example on the wiki page (and in the script) has -r - so the files are actually deleted from the disk by delete_datasets.sh. Does one still need to run purge_datasets.sh if used -r with delete_datasets.sh ? 4. If I accidentally run purge_datasets.sh without -r = is there a way to delete the stale files ? if not, perhaps the script should require either -i or -r to avoid such cases (or provide another cleanup script?) comments are welcomed, -gordon galaxy_cleanup_info_only.patch___ 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/ Greg Von Kuster Galaxy Development Team g...@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/
[galaxy-dev] Bam to fastq
Hi, Is there any way to convert a certain section of a bam file to fastq using the galaxy tools? I just want to convert a certain part of the genome. Thanks. Aaron ___ 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] Bam to fastq
Hi Aaron, On 07/06/2011 04:45 PM, Zschunke, Aaron M. wrote: Is there any way to convert a certain section of a bam file to fastq using the galaxy tools? I just want to convert a certain part of the genome. Thanks. there is the bam_to_fastq tool on the toolshed (http://toolshed.g2.bx.psu.edu/) in the SAM subsection. Regards, Holger -- Dr. Holger Klein Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de/ Tel: +49(6131) 39 21511 ___ 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] [galaxy-user] Fwd: deleting datasets from history
Hi, thank you for answer. I have tried to use the mentioned scripts but it seems that the order of their using at first time was incorrect.. As a result, the metadata in database tables are modified but the datasets files corresponded to deleted datasets in history remains unremoved. So, the following calling of the scripts in the right order (as indicated in wiki) also didn't delete the unused dataset files. Is there any way to update the metadata in tables according to the real state of files? I think that the order of calling the scripts at first time was the following: cleanup_datasets.py universe_wsgi.ini -d 1 -6 -r cleanup_datasets.py universe_wsgi.ini -d 6 -1 -r cleanup_datasets.py universe_wsgi.ini -d 2 -1 -r cleanup_datasets.py universe_wsgi.ini -d 3 -1 -r cleanup_datasets.py universe_wsgi.ini -d 4 -1 -r cleanup_datasets.py universe_wsgi.ini -d 5 -1 -r cleanup_datasets.py universe_wsgi.ini -d 1 -1 -r cleanup_datasets.py universe_wsgi.ini -d 1 -2 -r cleanup_datasets.py universe_wsgi.ini -d 1 -4 -r cleanup_datasets.py universe_wsgi.ini -d 1 -5 -r cleanup_datasets.py universe_wsgi.ini -d 1 -3 -r cleanup_datasets.py universe_wsgi.ini -d 1 -6 -r Also there are some strange things (imho) in galaxy.dataset table: there a lot of datasets id having or NULL total size: mysql select * from dataset where (id=148 or id=53 or id=86 or id=146 or id=330); +-+-+-+---+-++--+---+---+---++ | id | create_time | update_time | state | deleted | purged | purgable | external_filename | _extra_files_path | file_size | total_size | +-+-+-+---+-++--+---+---+---++ | 53 | 2011-03-29 16:21:58 | 2011-07-06 14:17:49 | error | 1 | 0 | 1 | NULL | NULL | 0 | NULL | | 86 | 2011-03-29 20:35:44 | 2011-07-06 14:17:52 | discarded | 1 | 0 | 1 | NULL | NULL | NULL | NULL | | 146 | 2011-05-26 01:38:14 | 2011-07-06 14:18:00 | error | 1 | 0 | 1 | NULL | NULL | NULL | NULL | | 148 | 2011-05-26 02:20:44 | 2011-07-06 14:18:00 | discarded | 1 | 0 | 1 | NULL | NULL | NULL | NULL | | 330 | 2011-07-05 00:44:44 | 2011-07-05 00:44:44 | NULL | 0 | 0 | 1 | NULL | NULL | NULL | NULL | +-+-+-+---+-++--+---+---+---++ I don't know how these records looked like before calling of the cleanup scripts, but is it possible that it is because of incorrect order of their calling? Is discarded state mean that the corresponded file should be deleted? But in my case all these files are still in database folder. Please, let me know if you need any other of clarification of my questions. 2011/7/6 Hans-Rudolf Hotz h...@fmi.ch Hi Sergei This is a question better asked on 'galaxy-...@bx.psu.edu' since you refer to your local Galaxy installation. In order to remove the data from your file system, you need to run the 'cleanup scripts', as described on this wiki page: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDatasets Regards, Hans On 07/06/2011 03:33 PM, Sergei Ryazansky wrote: Исходное сообщение Тема: deleting datasets from history Дата: Tue, 5 Jul 2011 19:58:45 +0300 От: Sergei Ryazansky s.ryazan...@gmail.com Кому: galaxy-user-requ...@lists.bx.psu.edu Hello all, After the deleating datasets from the history panel in our Galaxy mirror the indicator at the top right corner shows the same amount of used space as before deleting. Also, the files corresponded to the datasets remains in the Galaxy database/files/000 directory. It seems, that deleting of datasets from history is only delete the launch to file but not the file itself. How to configure the Galaxy mirror to delete not only records in history panel but also the corresponed files? Thank you in advance! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/
[galaxy-dev] adding qseq2fastq tool to the main instance
Hi, Is it possible to add the qseq2fastq tool developed by vipints (found under repositories) to the Galaxy web portal (the central server, not my own instance of Galaxy)? I believe this would be a popular tool used by many Illumina users? Best Regards, Mete Civelek IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. ___ 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] [galaxy-user] double login / deleting users
Joseph Hargitai wrote: Hi, 1, referencing old thread: http://gmod.827538.n3.nabble.com/Deleting-accounts-td867222.html is the delete functionality still status-quo? i.e - there is no delete other than the workaround? Hi Joe, Since this is regarding a local installation, I've moved this thread to the galaxy-dev list. I believe you still need the workaround, yes. 2, switched from SQLlite to postgres and have this strange double login issue. Included image - need to login twice and logout twice. Double tab - By any chance, are you using require_login = True in the config? Which logout link are you clicking to get to that page? Thanks, --nate joe ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/
[galaxy-dev] BAM display at Trackster
Hi Galaxy team, I am experiencing a problem with visualizing my BAM files through Trackster at my Galaxy instance. Please find the attached image along with this mail. From the log file I am not seeing any clues about the error message which is displayed on my browser page (A dependency (bai) was in an error state.) I updated my instance recently, It will be great if you can help me on the same. Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Tuebingen attachment: trackster_image_vipin.png___ 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] [galaxy-user] Fwd: deleting datasets from history
Assaf Gordon wrote: Hello Sergei, I'm experimenting with the clean-up scripts myself, so perhaps I can offer some information (the galaxy team is welcomed to correct me and/or explain better). 1. If you look at the output of your query, you'll notice that the purged field is 0 for all datasets (I assume 0 is false in MySQL). This means that the actual files where *not* purged (e.g. physically deleted) - at least not by the purge_datasets.sh or cleanup_datasets.py -3 step. Since you did use -r parameter, it means those dataset were not picked-up as possible deletion candidates by this script. 2. (The following I found by reading the source code, it's not really well explained - so if I'm wrong - correct me). The dataset table has an update_time field, and this field is updated automatically whenever the dataset record changes. This means that when you run the first cleanup script and set the deleted flag to true, the update_time is updated to now. When you run the next clean-up script and ask for anything that is older than 1 day (-d 1), it looks for the update_time older then one day - so it will *not* find the dataset that was just marked as deleted in the first step (because the update_time is now). Only if you run the next clean-up script tomorrow, that dataset will be deleted. So, for example, running the following in succession: cleanup_datasets.py universe_wsgi.ini -d 1 -6( = delete datasets ) cleanup_datasets.py universe_wsgi.ini -d 1 -3 -r ( = purge datasets + delete physical files) both run with -d 1 - but by design, files from yesterday (1 day old) will not be physically deleted. Files that the user deleted yesterday (1 day old) will be marked as deleted, but their update_time will by now. Only files that were marked as deleted yesterday will be deleted today (meaning: they are 2 days old). To really delete files now, use -d 0 with all the scripts. Since this is quite scary, the -i (info only) mode will show what what will be deleted (but that requires a recent version 5770:a5e0a5d3c0a1). 3. The file_size=NULL issue happen when a job fails - on some occasions (I couldn't pinpoint exactly when) galaxy does not pickup the fact the an output file was generated even if the job failed, and so you get ghost files which exist on the disk but are NULL in the database. The discard means the job was discarded (by the galaxy user?) - not that the dataset was deleted/purged by the clean-up scripts. Also, datasets created prior to the addition of the total_size column in changeset 5700:70e2b1c95a69 will have this unset - it can be set by running the script: % python ./scripts/set_dataset_sizes.py Also, Sergei, it's possible to allow users to force datsaets to be removed from disk after they delete them. See the 'allow_user_dataset_purge' option in universe_wsgi.ini. If set to True, users can select Show Deleted Datasets from the History's Options menu and then choose datasets to purge. Entire histories can be purged from the history list. --nate Hope this helps, -gordon Sergei Ryazansky wrote, On 07/06/2011 12:15 PM: Hi, thank you for answer. I have tried to use the mentioned scripts but it seems that the order of their using at first time was incorrect.. As a result, the metadata in database tables are modified but the datasets files corresponded to deleted datasets in history remains unremoved. So, the following calling of the scripts in the right order (as indicated in wiki) also didn't delete the unused dataset files. Is there any way to update the metadata in tables according to the real state of files? I think that the order of calling the scripts at first time was the following: cleanup_datasets.py universe_wsgi.ini -d 1 -6 -r cleanup_datasets.py universe_wsgi.ini -d 6 -1 -r cleanup_datasets.py universe_wsgi.ini -d 2 -1 -r cleanup_datasets.py universe_wsgi.ini -d 3 -1 -r cleanup_datasets.py universe_wsgi.ini -d 4 -1 -r cleanup_datasets.py universe_wsgi.ini -d 5 -1 -r cleanup_datasets.py universe_wsgi.ini -d 1 -1 -r cleanup_datasets.py universe_wsgi.ini -d 1 -2 -r cleanup_datasets.py universe_wsgi.ini -d 1 -4 -r cleanup_datasets.py universe_wsgi.ini -d 1 -5 -r cleanup_datasets.py universe_wsgi.ini -d 1 -3 -r cleanup_datasets.py universe_wsgi.ini -d 1 -6 -r Also there are some strange things (imho) in galaxy.dataset table: there a lot of datasets id having or NULL total size: mysql select * from dataset where (id=148 or id=53 or id=86 or id=146 or id=330); +-+-+-+---+-++--+---+---+---++ | id | create_time | update_time | state | deleted | purged | purgable | external_filename | _extra_files_path | file_size | total_size |
Re: [galaxy-dev] [galaxy-user] double login / deleting users
Joseph Hargitai wrote: 2, switched from SQLlite to postgres and have this strange double login issue. Included image - need to login twice and logout twice. Double tab - By any chance, are you using require_login = True in the config? Which logout link are you clicking to get to that page? -- 1, yes, it is set to True. 2, when i hit logout, the secondary galaxy appears in the window (now 2 menu bars) The message is you are logged out - and the options are in this inner Galaxy bar, Login/Register. The top bar still has me as logged in and allows for a logout. When I do, it does log me out. Okay, this is probably a bug with using require_login. You should find that you are actually logged out, but the masthead has not refreshed. I've filed a bug report here: https://bitbucket.org/galaxy/galaxy-central/issue/598/logout-loads-in-the-center-panel-and-does 3, do I need to remove remnants of SQLlite in /databases? No, this is not necessary. --nate joe ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/
[galaxy-dev] Hidden history item
Hi all, by default I let my tools produce (the old way) a logfile of the console and additional running statistics. This is convenient at tool setup and ocassionally for troubleshooting. Anyway I would like to make the corresponding history item hidden. I tried including hidden=true in the output tag but that does not make any difference. Is this possible at all or only applicable to running workflows? Any pointers appreciated. Alex ___ 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] bug or feature :)
In our local instance (central version) up to changeset (June 28th) I noticed in the admin panel to manage jobs some odd behaviour; When I set the update Jobs cutoff on 10 seconds and press refresh the item below (administrative Job Lock) is also activated and new jobs are locked. Is that a planned feature, a bug or is something wrong in our local instance. Another refresh toggles it back to normal. Alex ___ 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] [galaxy-user] Fwd: deleting datasets from history
Hello Assaf, thank you for the exellent explanation, the situation is become more clearly for me. 06.07.2011 21:19, Assaf Gordon пишет: Hello Sergei, I'm experimenting with the clean-up scripts myself, so perhaps I can offer some information (the galaxy team is welcomed to correct me and/or explain better). 1. If you look at the output of your query, you'll notice that the purged field is 0 for all datasets (I assume 0 is false in MySQL). This means that the actual files where *not* purged (e.g. physically deleted) - at least not by the purge_datasets.sh or cleanup_datasets.py -3 step. Since you did use -r parameter, it means those dataset were not picked-up as possible deletion candidates by this script. 2. (The following I found by reading the source code, it's not really well explained - so if I'm wrong - correct me). The dataset table has an update_time field, and this field is updated automatically whenever the dataset record changes. This means that when you run the first cleanup script and set the deleted flag to true, the update_time is updated to now. When you run the next clean-up script and ask for anything that is older than 1 day (-d 1), it looks for the update_time older then one day - so it will *not* find the dataset that was just marked as deleted in the first step (because the update_time is now). Only if you run the next clean-up script tomorrow, that dataset will be deleted. So, for example, running the following in succession: cleanup_datasets.py universe_wsgi.ini -d 1 -6( = delete datasets ) cleanup_datasets.py universe_wsgi.ini -d 1 -3 -r ( = purge datasets + delete physical files) both run with -d 1 - but by design, files from yesterday (1 day old) will not be physically deleted. Files that the user deleted yesterday (1 day old) will be marked as deleted, but their update_time will by now. Only files that were marked as deleted yesterday will be deleted today (meaning: they are 2 days old). To really delete files now, use -d 0 with all the scripts. Since this is quite scary, the -i (info only) mode will show what what will be deleted (but that requires a recent version 5770:a5e0a5d3c0a1). 3. The file_size=NULL issue happen when a job fails - on some occasions (I couldn't pinpoint exactly when) galaxy does not pickup the fact the an output file was generated even if the job failed, and so you get ghost files which exist on the disk but are NULL in the database. The discard means the job was discarded (by the galaxy user?) - not that the dataset was deleted/purged by the clean-up scripts. Hope this helps, -gordon Sergei Ryazansky wrote, On 07/06/2011 12:15 PM: Hi, thank you for answer. I have tried to use the mentioned scripts but it seems that the order of their using at first time was incorrect.. As a result, the metadata in database tables are modified but the datasets files corresponded to deleted datasets in history remains unremoved. So, the following calling of the scripts in the right order (as indicated in wiki) also didn't delete the unused dataset files. Is there any way to update the metadata in tables according to the real state of files? I think that the order of calling the scripts at first time was the following: cleanup_datasets.py universe_wsgi.ini -d 1 -6 -r cleanup_datasets.py universe_wsgi.ini -d 6 -1 -r cleanup_datasets.py universe_wsgi.ini -d 2 -1 -r cleanup_datasets.py universe_wsgi.ini -d 3 -1 -r cleanup_datasets.py universe_wsgi.ini -d 4 -1 -r cleanup_datasets.py universe_wsgi.ini -d 5 -1 -r cleanup_datasets.py universe_wsgi.ini -d 1 -1 -r cleanup_datasets.py universe_wsgi.ini -d 1 -2 -r cleanup_datasets.py universe_wsgi.ini -d 1 -4 -r cleanup_datasets.py universe_wsgi.ini -d 1 -5 -r cleanup_datasets.py universe_wsgi.ini -d 1 -3 -r cleanup_datasets.py universe_wsgi.ini -d 1 -6 -r Also there are some strange things (imho) in galaxy.dataset table: there a lot of datasets id having or NULL total size: mysql select * from dataset where (id=148 or id=53 or id=86 or id=146 or id=330); +-+-+-+---+-++--+---+---+---++ | id | create_time | update_time | state | deleted | purged | purgable | external_filename | _extra_files_path | file_size | total_size | +-+-+-+---+-++--+---+---+---++ | 53 | 2011-03-29 16:21:58 | 2011-07-06 14:17:49 | error | 1 | 0 | 1 | NULL | NULL | 0 | NULL | | 86 | 2011-03-29 20:35:44 | 2011-07-06 14:17:52 | discarded | 1 | 0 | 1 | NULL | NULL | NULL | NULL | | 146 | 2011-05-26 01:38:14 | 2011-07-06 14:18:00 | error | 1 | 0 | 1 | NULL | NULL | NULL | NULL | | 148 | 2011-05-26 02:20:44 | 2011-07-06 14:18:00 | discarded | 1 | 0 | 1 | NULL | NULL | NULL | NULL | | 330 | 2011-07-05 00:44:44 | 2011-07-05 00:44:44 | NULL | 0 | 0 | 1 |
Re: [galaxy-dev] [galaxy-user] Fwd: deleting datasets from history
Thanks for reply! set_dataset_sizes.py works fine for me. By the way, what is difference between file_size and total_size fields? It seems that their values are equal. Although 'allow_user_dataset_purge' setting seems to be very usefull, but it is absent in my universe_wsgi.ini file (galaxy_dist). 06.07.2011 22:28, Nate Coraor пишет: Also, datasets created prior to the addition of the total_size column in changeset 5700:70e2b1c95a69 will have this unset - it can be set by running the script: % python ./scripts/set_dataset_sizes.py Also, Sergei, it's possible to allow users to force datsaets to be removed from disk after they delete them. See the 'allow_user_dataset_purge' option in universe_wsgi.ini. If set to True, users can select Show Deleted Datasets from the History's Options menu and then choose datasets to purge. Entire histories can be purged from the history list. --nate ___ 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] Several errors from run.sh
Hi all, I am upgrading to the most recent galaxy-dist 720455407d1chttps://bitbucket.org/galaxy/galaxy-dist/changeset/720455407d1c . First time run.sh shows following errors as in attachment. It seems when I use 'manage_db.sh upgrade' it doesn't create necessary tables for these tools. Wonder if these are known issues? Thanks [epigraph] galaxy.tools ERROR 2011-07-05 10:34:12,556 error reading tool from path: data_destination/epigraph.xml Traceback (most recent call last): File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 169, in load_tool return ToolClass( config_file, root, self.app ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 340, in __init__ self.parse( root ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 385, in parse self.interpreter = command.get(interpreter, None) AttributeError: 'NoneType' object has no attribute 'get' galaxy.tools ERROR 2011-07-05 10:34:12,559 error reading tool from path: data_destination/epigraph_test.xml Traceback (most recent call last): File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 169, in load_tool return ToolClass( config_file, root, self.app ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 340, in __init__ self.parse( root ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 385, in parse self.interpreter = command.get(interpreter, None) AttributeError: 'NoneType' object has no attribute 'get' [manipulation] galaxy.tools WARNING 2011-07-05 10:34:16,151 A when tag has been defined for 'manipulation (manipulation_selector) -- modify_each_score', but does not appear to be selectable. [picard] galaxy.tools ERROR 2011-07-05 10:34:16,700 error reading tool from path: picard/picard_ReorderSam.xml Traceback (most recent call last): File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 169, in load_tool return ToolClass( config_file, root, self.app ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 340, in __init__ self.parse( root ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 441, in parse self.parse_inputs( root ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 523, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 703, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 770, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 796, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 808, in parse_param_elem param = ToolParameter.build( self, input_elem ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py, line 161, in build return parameter_types[param_type]( tool, param ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py, line 607, in __init__ self.options = dynamic_options.DynamicOptions( options, self ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py, line 411, in __init__ Data table named '%s' is required by tool but not configured % tool_data_table_name AssertionError: Data table named 'picard_indexes' is required by tool but not configured [mosaik] galaxy.tools ERROR 2011-07-05 10:34:17,217 error reading tool from path: sr_mapping/mosaik.xml Traceback (most recent call last): File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 169, in load_tool return ToolClass( config_file, root, self.app ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 340, in __init__ self.parse( root ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 441, in parse self.parse_inputs( root ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 523, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File /home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py, line 703, in parse_input_page inputs = self.parse_input_elem(
[galaxy-dev] Error in running
Hello, My name is Dayananda Sagar Gangadharaiah and I am a computational biology research associate at the University of Nebraska, Lincoln. We have been trying to install Galaxy for running a software tool called KIRMES. We are encountering the following errors when we run Galaxy using sh ./run.sh command *ERROR: Unable to read builds file: [Errno 2] No such file or directory: '/mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared * */ucsc/builds.txt'* *ERROR: Unable to read builds for site file /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/ucsc/ucsc_build_sites.txt * *ERROR: Unable to read builds for site file /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/gbrowse/gbrowse_build_sites.t * *xt* *ERROR: Unable to read builds for site file /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/util/../../../tool-data/shared/genetrack/genetrack_sites.txt * *python path is: /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs2.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/* *pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs2.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg, /mnt/nfs/software/pkgs/* *TFBS/galaxy/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs2.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-li * *nux-x86_64-ucs2.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1-py2.6-linux-x86_64-ucs2.egg, /mnt/nfs/software/pkg* *s/TFBS/galaxy/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/ga* *laxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /mnt/nfs/software/pkgs/TFB* *S/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs2.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /mnt/nfs/softwar* *e/pkgs/TFBS/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg, /* *mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6. * *egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /mnt/* *nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2 * *.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.* *6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib, /arch/lib/python2.6/site-pack* *ages/setuptools-0.6c11-py2.6.egg, /arch/lib/python2.6/site-packages/pip-1.0.1-py2.6.egg, /arch/lib/python26.zip, /arch/lib/python2.6, /arch/lib/python2.6/plat-li* *nux2, /arch/lib/python2.6/lib-tk, /arch/lib/python2.6/lib-old, /arch/lib/python2.6/lib-dynload, /mnt/nfs/software/software/64-bit/lib/python2.6/site-packages* *Traceback (most recent call last):* * File /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 82, in app_factory* *app = UniverseApplication( global_conf = global_conf, **kwargs )* * File /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/app.py, line 20, in __init__* *self.config.check()* * File /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/lib/galaxy/config.py, line 174, in check* *raise ConfigurationError(Directory does not exist: %s % path )* *ConfigurationError: Directory does not exist: /mnt/nfs/software/pkgs/TFBS/galaxy/galaxy-dist/tool-data* Since we do not work on Python we are not able to rectify these problems. Please help us in fixing these errors. Regards, Dayananda Sagar Gangadharaiah E115, Beadle Center University of Nebraska- Lincoln 1901 Vine St., Lincoln, NE 68588-0665 Phone: (402) 472-8236 ___ 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] rgWebLogo3 with Probabilities instead of Entropy
FYI: I patched the wrapper to offer all the weblogo Y axis scale options and an additional test to central #5766 and some additional dependency error reporting in #5772 - latest wrapper version is 0.4 On Fri, Jul 1, 2011 at 8:28 AM, Ross ross.laza...@gmail.com wrote: Thanks - code to accompany good suggestions is always appreciated :) I'll write a test and get a patched version on test as soon as I get some time - travelling all day today - will let you know when it's done On Fri, Jul 1, 2011 at 7:20 AM, Assaf Gordon gor...@cshl.edu wrote: Hello Ross and Galaxy team, May I suggest this small patch, that enables WebLogo to plot either Entropy bits (the current default) or just nucleotides probabilities ? It uses the standard -U parameter of weblogo3. -gordon ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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] suggestions for the SAM-to-BAM tool
Hello - We haven't forgotten about these suggestions and still plan on working a least a few of them (Kelly would know more). I decided to put them into a bitbucket ticket for easier tracking: http://bitbucket.org/galaxy/galaxy-central/issue/601 Many thanks, as always, for the feedback! Best, Jen Galaxy team On 4/1/11 11:39 AM, Assaf Gordon wrote: Hi, Couple of things that can be slightly improved in the SAM-to-BAM tool: 1. Reference list is not informative (it's the technical way to say: list of chromosomes and their sizes based on a FASTA file). Users do not generally know what reference list is. 2. The Locally Cached option is not informative (I had to look in the source code to understand what it means). What it should say is something like: Get list of chromosomes/sizes based on the dataset's organism/database (could be shorter, but should be friendly enough). 3. There's no option of having the chromosome list in the SAM file header. Some SAM files will contain the header (can even be done in the standard bowtie tool wrapper) - saves the need to specify where to get the reference list from. 4. Autodetection in the set-metadata step will go a long way here: if the SAM file already have a header, then no need to even ask about it. If it doesn't have a header but have a DBKEY, then we're still OK. If no DBKEY and no header, then complain or ask for a FASTA file from current history. (I realize the implementing this feature is hard and annoying, I don't imply that it's easy to do, just that it's needed). 5. Inside the python script (sam_to_bam.py) there's a comment that says: for some reason the samtools view command gzips the resulting bam file without warning . Not sure why one cares about that, but samtools view -u will output an uncompressed BAM file. 6. samtools support piping, so a lot of I/O (and some time) can be spared by piping the two commands together: samtools view -u -b -S INPUT.SAM | samtools sort - OUTPUT Instead of running two commands and generating a temporary unsorted BAM file. -gordon ___ 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/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ ___ 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/
