May 2013 - galaxy-dev - lists.galaxyproject.org

Cross Tool Shed dependencies / blast_datatypes
by Peter Cock 25 May '13

25 May '13

Hi Greg, Do you guys have a rough plan for when inter-ToolShed dependencies will be supported? I've been using the Test Tool Shed to validate tools before uploading them to the main Tool Shed - this uncovers things like omitted test files which I don't find locally since I'm testing in-situ. Right now the single biggest class of test failures amongst my tools on the Test Tool Shed is a missing dependencies on the blast_datatypes repository: http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes As a short term measure, could the dev team upload blast_datatypes to the Test Tool Shed as well please (and give me write access)? Then thanks to the recent change in [1] I can reference the dependency without explicitly naming the Tool Shed. If you can do it in a way that preserves the same revision history can change set hashes even better - then I can replace this: <repository toolshed="http://toolshed.g2.bx.psu.edu" name="blast_datatypes" owner="devteam" changeset_revision="f9a7783ed7b6" /> with: <repository name="blast_datatypes" owner="devteam" changeset_revision="f9a7783ed7b6" /> and can use the same repository_dependencies.xml file on both Tool Sheds. If preserving the hashes isn't possible, I'll use the new [2] 'latest revision' ability instead: <repository name="blast_datatypes" owner="devteam" /> Thanks, Peter -- [1] https://bitbucket.org/galaxy/galaxy-central/commits/842a78530fcd87670198d55… [2] https://bitbucket.org/galaxy/galaxy-central/commits/35de5a8a928bf63fd5de3d1…

3 11

Problem with ftp connexion to Galaxy
by Fabrice BESNARD 24 May '13

24 May '13

Hello, I am a new Galaxy User. I am definitely not an expert in informatics, so my questions may sound silly to you... I apologize if it is the case! Anyway, I cound not establish a ftp connexion to Galaxy through Filezilla, and the error message suggests that it comes from an incorrect password to Galaxy. Here is the messages displayed by Filezilla (french version) while trying to connnect: Statut : Résolution de l'adresse de main.g2.bx.psu.edu Statut : Connexion à 128.118.250.4:21... Statut : Connexion établie, attente du message d'accueil... Réponse : 220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP) [::ffff:128.118.250.4] Commande : USER fbesnard(a)biologie.ens.fr Réponse : 331 Password required for fbesnard(a)biologie.ens.fr Commande : PASS *************** Réponse : 530 Login incorrect. Erreur : Erreur critique Erreur : Impossible d'établir une connexion au serveur I was puzzled by this error message, because I do connect as user in the Galaxy website. As recommended, I use the SAME login (=email adress)/Password in both Galaxy login page and filezilla. I tried to reset my password and connect again: I could connect directly to the web site, but I still failed establishing a connexion via filezilla. I just created an account yesterday to Galaxy (Tuesday, 21th of May 2013). Maybe I should just wait a little bit for a synchronization of the user connexion parameters, should I? Moreover, my Filezilla is working with other ftp server, so that I think we can exclude that the problem comes from there. I extensively looked for similar trouble reports on internet (googling with other terms "530 Login incorrect"). Unfortunately, I could not solve this problem. However, I found that you were asked one year ago for a similar problem in this page: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-July/010457.html But I must confess that I could not understand most of what was written in this informatic experts discussion! By the way, my system is not an ubuntu, so I think that the solution you suggested would not work in my case. Here are the characteristics and versions of the systems installed on my computer: Operating system: Windows 7 professionnal, 64bits Filezilla Client 3.7.0.1 Firefox 20.0.1 I really thank you for reading this help message and I hope that you could explain me how to solve my problem. I look forward to reading your answer soon, Best regards, -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesnard(a)biologie.ens.fr Tel: +33-1-44-32-39-44

2 1

Problem about main.g2.bx.psu.edu is taking too long to respond.
by จุรีรัตน์ โพธิ์แก้ว 24 May '13

24 May '13

Dear Galaxy team, I have problem with my galaxy because I can 't check my data. I refresh my page several time but it keep report the connection has timed out. Please let me know what should I do to fix this problem. Thanks, Chureerat

2 1

populating the pull-down menu: reference genomes (built-in index)
by Staheli, Jeannette 24 May '13

24 May '13

Hi, We are trying to put a few reference genomes into the built-in index for bwa, bowtie, bowtie2 and tophat. For the human hg19 we can find those. However, we also like to upload the Rhesus macaque genome and haven't been able to find an indexed version at NCBI or other places. Are other genomes pre-indexed for these applications somewhere? How do those files look like exactly (extensions, number of files needed, etc.)? How would we index the Rhesus genome for the above mappers if they are not available in an indexed form? Thank you, Jeannette CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

2 1

Problem to download mercurial egg
by Jennifer Jackson 24 May '13

24 May '13

Moving the question over to development list http://wiki.galaxyproject.org/MailingLists -------- Original Message -------- Subject: [galaxy-user] Problem to download mercurial egg Date: Fri, 24 May 2013 14:17:11 +0200 From: Marc DELOGER <marc.deloger(a)igr.fr> To: <galaxy-user(a)lists.bx.psu.edu> Hello, I tried to download several times the several egg on these following mirrors but the download is always blocked near 50%...I asked several different people and they all have the same problem : http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4… <http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4…> http://eggs.galaxyproject.org/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-… <http://eggs.galaxyproject.org/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-…> Thank you in advance, Marc DELOGER -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

1 0

liftover
by Anna Kropornicka 24 May '13

24 May '13

Good afternoon, I was wondering if I could get some help on the installation of the liftover tool from UCSC. I was able to modify the liftOver.loc and downloaded some over.chain files from UCSC to the appropriate folder. I believe the problem extends from not having a liftover folder in my 'tools' folder. I downloaded a local copy of galaxy called "galaxy-dist" and have made sure it's up to date. Thank you, Anna Kropornicka kropornicka(a)wisc.edu Department of Genetics University of Wisconsin-Madison Biochemistry Addition 433 Babcock Drive, Rm 319 Madison, WI 53706 tel: (608) 262-4550x3140

1 0

Is there a way through the API to know when a file has completed the upload process?
by Anthonius deBoer 24 May '13

24 May '13

Hi, I am trying to use the API to upload a file and since the upload can take a long time (see my previous post) I need to check if the upload has completed so I know I can start a workflow (or can I start a workflow even when the file is still in the "queued" state?)... I have successfully used the examples from this page: http://galaxy-dist.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.… and can easily upload a file, but I cannot seem to learn the state of the file... The upload process I used, returned a bunch of attributes, such as: {'ldda_id': '049d723a33542847', 'misc_blurb': None, 'name': '7_101_1_ACTTGA_R1.fastq', 'data_type': 'fastq', 'file_name': '/mnt/ngs/analysis/tdeboer/PROJECTS/STAGING/SEQUENCER07/130207_SN7001380_0101_AD1H7GACXX/fastq/7_101_1_ACTTGA_R1.fastq', 'uploaded_by': 'tdeboer(a)genomichealth.com', 'metadata_sequences': None, 'template_data': {}, 'genome_build': 'hg19', 'model_class': 'LibraryDataset', 'misc_info': None, 'file_size': 6410080411, 'metadata_data_lines': None, 'message': '', 'id': '049d723a33542847', 'date_uploaded': '2013-05-22T00:50:50.474318', 'metadata_dbkey': 'hg19'} But none of those tell me if the upload has succeeded or not... Is there a way to retrieve the state of an uploaded file once I have uploaded a file through the API? thanks Thon

2 1

Displaying genomic sequences in Trackster
by Naharajan Lakshmanaperumal 24 May '13

24 May '13

Dear all, We have our own galaxy instance and the idea is to have trackster enabled for users to be able to visualize NGS mapping. We were able to configure trackster in our instance and the visualization works fine. We have two questions regarding trackster: 1) We can't display genomic sequences in trackster. As per the tutorial, we set the location of the .2bit file in the twobit.loc file for the trackster to be able to display the genomic sequence but for some reason it doesn't display it. The name of the builds is the same in all places i.e) in ucsc/chrom/builds.txt and also in the .loc files. Any ideas on what else should be done? 2) While saving the visualization, there is always an error message saying "could not save visualization" and it doesn't seem to be a web browser issue. How do we then save the visualization? Thanks in advance, Naharajan

3 4

XML files for MACS v1.4
by vijayalakshmi 23 May '13

23 May '13

HI all, I am trying to integrate MACS v1.4 into Galaxy. But I am unable to find the XML for the following MACS tools 1) elandexport2bed 2) elandmulti2bed 3) elandresult2bed 4) macs14 5) sam2bed 6) wignorm Any pointer/guidance is appreciated. Thanks, VJ.

1 0

Suggestion for "Latest revision: installation errors"
by Peter Cock 23 May '13

23 May '13

Hi Greg, I think it would be useful to be a little more inclusive on the Tool Shed listing "Latest revision: installation errors" and include repositories with tools missing tests, e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/2d4757de6180 Some of the BLAST+ tools don't yet have tests (since they require functionality not yet supported), but at that revision at least there is also an installation error - which we're discussing here: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014795.html On a related point, it would be good to have the RSS feeds mention installation errors. Thanks, Peter

2 1