April 2012 - galaxy-dev - lists.galaxyproject.org

Default annotation track
by Oleksandr Moskalenko 19 Apr '12

19 Apr '12

I needed to add a genome to the tracks in our local instance. However, the only available genome is a multi-fasta file of about 1800 supercontigs. I preserve the sanity of my clients I concatenated the fasta file and provided both versions. The unfortunate part is that the contig annotation data is lost in that conversion. I wonder if there is a way to extract the contig data as annotation and provide it as a default track in the concatenated genome or something like that. Any ideas? Thanks, Alex

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Error copying files from job_working_directory
by Jose Navas 19 Apr '12

19 Apr '12

Hello, I've integrated a tool into my Galaxy instance, but when I run the tool I get this error: galaxy.objectstore CRITICAL 2012-04-16 11:25:56,697 Error copying /home/galaxy/galaxy-dist/database/job_working_directory/000/307/dataset_431_files/unweighted_unifrac_2d_continuous to /home/galaxy/galaxy-dist/database/files/000/dataset_431_files/unweighted_unifrac_2d_continuous: [Errno 21] Is a directory: '/home/galaxy/galaxy-dist/database/job_working_directory/000/307/dataset_431_files/unweighted_unifrac_2d_continuous' As I can see, it fails because it is trying to copy a directory. Is this feature supported in Galaxy? If it is supported, what I have to do to enable copy the directories from the job_working_directory? Thank you, Jose

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Error running set_dataset_sizes.py
by Liisa Koski 19 Apr '12

19 Apr '12

Hello, I'm seeing some discrepancies in total user usage versus what my histories actually total so I wanted to run set_dataset_sizes.py and set_user_disk_usage.py I am getting the following error. ./set_dataset_sizes.py Loading Galaxy model... Processing 77915 datasets... Completed 0% Traceback (most recent call last): File "./set_dataset_sizes.py", line 43, in <module> dataset.set_total_size() File "lib/galaxy/model/__init__.py", line 703, in set_total_size if self.object_store.exists(self, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True): AttributeError: 'NoneType' object has no attribute 'exists' Any help would be much appreciated. Thanks, Liisa

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delete data library via API
by Leon Mei 19 Apr '12

19 Apr '12

Hi guys, Is that possible to delete datasets in a shared data library via API? Of course when the modify permission is granted. We see delete.py in the API script folder but can't figure out how to get it work. Thanks! Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nl<https://wiki.nbic.nl/index.php/Next_Generation_Sequencing> Skype: leon_mei Mobile: +31 6 41709231

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Re: [galaxy-dev] Problem with cleaning up galaxy datasets
by Jennifer Jackson 19 Apr '12

19 Apr '12

repost bounced msg, see why below --------- Date: Sat, 14 Apr 2012 22:33:22 +0200 From: Klaus Metzeler <mail(a)klaus-metzeler.de> To: Michael Moore <michaelglennmoore(a)gmail.com> Cc: galaxy-dev(a)lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem with cleaning up galaxy datasets Message-ID: <4F89DF12.6010606(a)klaus-metzeler.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed OK, this pointed me to the right direction. The universe_wsgi.ini file has a key that reads: database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE This entry was commented out in my version of the file (ie, had a # in front of it). While Galaxy itself uses this database connection by default, but the cleanup script looks for this config file entry to locate the database. So, if anyone encounters the same problem, just un-comment this entry and all runs fine. Thanks for your help, Michael. -- Why did this bounce? Digest content not stripped (#2). If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Thanks Klaus for sending in the solution! - Galaxy team -- Jennifer Jackson http://galaxyproject.org

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Copying galaxy folder from linux to windows
by diana michelle magbanua 19 Apr '12

19 Apr '12

Hi there, Since manually deleting the files from the galaxy database is not advised, I thought of just copying the galaxy-dist folder from the linux server to my windows. I copied everything except the 000 folder, where the datasets are located. I also have Cygwin installed in windows. I was wondering if galaxy would still run even if I just copied the folder. About my dataset cleanup problem: I tried running the cleanup scripts, but since the disk is full I cannot make any changes to universe_wsgi.ini (I get this KeyError problem). Any suggestions on how I could free some space/delete datasets? Is manually deleting tmp files also not advised? I am not allowed to remove/alter any other file aside from those within galaxy-dist. Any help would be greatly appreciated. Cheers, DM

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Deleting datasets from server
by diana michelle magbanua 19 Apr '12

19 Apr '12

Hi there, I would just like to ask if I could just directly delete the .dat files from the database folder of Galaxy (or even just the tmp files). I am not allowed to delete any other file from the computer other than the ones in galaxy-dist. I have tried running the cleanup scripts, but since the disk is already full, I am experiencing some problems with the cleanup. I'm just new to using this application, so any help would greatly be appreciated. Cheers, Michelle

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Cuffdiff output
by Xu, Jianpeng 18 Apr '12

18 Apr '12

Hi, I have ran Cuffdiff and got output files: transcript differential expression testing, gene differential expression testing. Could you please tell me how to get the significant differential expression gene and transcript ? Thanks, ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Private key file format issue (for connecting EC2 instance with EBS volume)
by Mohammad Heydarian 18 Apr '12

18 Apr '12

Hello, I am trying to connect an EC2 instance to an EBS volume. I have attached the EBS volume to the EC2 instance (running Galaxy). I now need to mount the EBS volume to the EC2 instance. To do this I will use Putty to make the connection. But first I have to convert the private key from ".pem" format to ".ppk" format. I am trying to use Puttygen for the conversion, but the ".pem" file is not recognized and I get this error message: Could't load private key (key file does not begin with OpenSSH key header) Does anyone have experience with this? BTW, I am using windows. Thanks! Cheers, Mo Heydarian

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Moving data about the EC2/EBS/S3 spaces on the Amazon cloud.
by Mohammad Heydarian 18 Apr '12

18 Apr '12

Hello, I am new to cloud computing and am trying to use the Galaxy cloudman service through Amazon to analyse NGS data. I have a couple of questions regarding data transfer: If I am running an EC2 instance, with an EBS volume attached, how can I retrieve the data from the EBS volume? In addition, how do I view what files are in the EBS volume? Can I send the data to an S3 bucket? And how would I move data from the S3 bucket to a fresh EC2 instance? Assuming I can store my files on EBS (or S3), what is the best way to download them? Can I set up a ftp transfer to (quickly) download my potentially very large files? Many thanks for any insight and direction! Cheers, Mo Heydarian

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