Re: [galaxy-dev] Set a FTP upload in Local Galaxy instance
Hi Thomas, How do you ensure that files are created with galaxy ownership using the samba share? Regards, Iyad Kandalaft Bioinformatics Programmer Microbial Biodiversity Bioinformatics Science & Technology Branch Agriculture & Agri-Food Canada iyad.kandal...@agr.gc.ca | (613) 759-1228 From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Thomas Bellembois [thomas.bellemb...@ens-lyon.fr] Sent: July 1, 2014 5:44 AM To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Set a FTP upload in Local Galaxy instance Hi Pat, At the ENS we use a Samba share. This is an alternate solution. Our /opt/galaxy-dist/database/upload folder contains a subfolder per user (usern...@ens-lyon.fr). Regards, Thomas -- Thomas Bellembois, Network and System Administrator ENS-Lyon/IGFL - FRANCE +33 4 26 73 13 67 .The IGFL is a member of the "portail-labos" project (https://portail-labos.ens-lyon.fr/site/). .IGFL IT documentation: http://itdoc.igfl.ens-lyon.fr/itdoc On 30/06/2014 02:41, Kandalaft, Iyad wrote: > Hi Pat, > > Briefly, to get galaxy uploads working, you need to do the following: > > 1. Install an FTP server. The FTP server can be on the same/different host > than galaxy but must be able to access the "ftp_upload_dir" > 2. Configure the FTP server to authenticate users. This needs to be the same > user ID as the galaxy user ID. For example: user id -> > iyad.kandal...@agr.gc.ca > 3. Configure the FTP server to create a folder in "ftp_upload_dir" that has > the same name as the user that logged into the FTP server. For example: user > id -> iyad.kandal...@agr.gc.ca directory is -> > galaxy_dist/database/files/iyad.kandal...@agr.gc.ca/ > > > The link you posted takes briefly describes how to configure ProFTPd, which > is an FTP server, to work with Galaxy. Unfortunately, the page is somewhat > random as it describes steps for some operating systems in detail but leaves > out the details for other operating systems. > > On a redhat/centos operating systems, you install proftpd using: > > sudo yum install proftpd > > On Debian/Ubuntu: > > sudo apt-get install proftpd > > The configuration file that the tutorial refers to is /etc/proftpd.conf > > I hope this helps get you started. > > Regards, > > Iyad Kandalaft > Bioinformatics Programmer > Microbial Biodiversity Bioinformatics > Science & Technology Branch > Agriculture & Agri-Food Canada > iyad.kandal...@agr.gc.ca | (613) 759-1228 > > From: galaxy-dev-boun...@lists.bx.psu.edu > [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Pat-74100 > [leonardsqual...@hotmail.com] > Sent: June 29, 2014 10:29 AM > To: galaxy-dev@lists.bx.psu.edu > Subject: [galaxy-dev] Set a FTP upload in Local Galaxy instance > > Dear Galaxy developers > > I'm trying to allow users to upload file via FTP. > > I've been to the tutorial website but as a beginner, I understand nothing... > > https://wiki.galaxyproject.org/Admin/Config/UploadviaFTP?action=show&redirect=Admin%2FConfig%2FUpload+via+FTP > > I've configured the universe_wsgi.ini file with > > ftp_upload_dir = galaxy_dist/database/files/ > ftp_upload_site = any adress. > > I use Filezilla to for FTP connecting but it doesn't works and it asks me a > Port ... > Can someone provide to me a simply tutorial to enable ftp upload ? > > Thanks > > Pat > > ___ > 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/ ___ 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] Tophat for illumina reference genome
Hello, I've recently set up a local instance of galaxy in our office. I've downloaded the data mangers for Bowtie and Bowtie 2 and have been able to use these to index the reference genomes for both these tools. However our tophat for illumina and tophat 2 installations do not show any reference genomes. I was under the impression that these tools used the same genomes as Bowtie and Bowtie 2 respectively and thought that the data managers would also index the genomes for these tools. Is this correct or will I need to set the indexes up manually using the .loc files? Thanks, Findlay. ___ 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] ImportError: No module named galaxy_utils.sequence.fastq
Hi, I've this error message when I run groomer. My local instance of galaxy runs on a python virtualenv (python 2.7) and I have make the latest update with : hg pull -u. I've verified and this library is present in my galaxy-dist/lib/galaxy_utils/sequence directory. I've found no other idea than the update on this forum to run groomer correctly, any other idea ? Thanks. Julie ___ 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] Set a FTP upload in Local Galaxy instance
Hi Pat, At the ENS we use a Samba share. This is an alternate solution. Our /opt/galaxy-dist/database/upload folder contains a subfolder per user (usern...@ens-lyon.fr). Regards, Thomas -- Thomas Bellembois, Network and System Administrator ENS-Lyon/IGFL - FRANCE +33 4 26 73 13 67 .The IGFL is a member of the "portail-labos" project (https://portail-labos.ens-lyon.fr/site/). .IGFL IT documentation: http://itdoc.igfl.ens-lyon.fr/itdoc On 30/06/2014 02:41, Kandalaft, Iyad wrote: > Hi Pat, > > Briefly, to get galaxy uploads working, you need to do the following: > > 1. Install an FTP server. The FTP server can be on the same/different host > than galaxy but must be able to access the "ftp_upload_dir" > 2. Configure the FTP server to authenticate users. This needs to be the same > user ID as the galaxy user ID. For example: user id -> > iyad.kandal...@agr.gc.ca > 3. Configure the FTP server to create a folder in "ftp_upload_dir" that has > the same name as the user that logged into the FTP server. For example: user > id -> iyad.kandal...@agr.gc.ca directory is -> > galaxy_dist/database/files/iyad.kandal...@agr.gc.ca/ > > > The link you posted takes briefly describes how to configure ProFTPd, which > is an FTP server, to work with Galaxy. Unfortunately, the page is somewhat > random as it describes steps for some operating systems in detail but leaves > out the details for other operating systems. > > On a redhat/centos operating systems, you install proftpd using: > > sudo yum install proftpd > > On Debian/Ubuntu: > > sudo apt-get install proftpd > > The configuration file that the tutorial refers to is /etc/proftpd.conf > > I hope this helps get you started. > > Regards, > > Iyad Kandalaft > Bioinformatics Programmer > Microbial Biodiversity Bioinformatics > Science & Technology Branch > Agriculture & Agri-Food Canada > iyad.kandal...@agr.gc.ca | (613) 759-1228 > > From: galaxy-dev-boun...@lists.bx.psu.edu > [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Pat-74100 > [leonardsqual...@hotmail.com] > Sent: June 29, 2014 10:29 AM > To: galaxy-dev@lists.bx.psu.edu > Subject: [galaxy-dev] Set a FTP upload in Local Galaxy instance > > Dear Galaxy developers > > I'm trying to allow users to upload file via FTP. > > I've been to the tutorial website but as a beginner, I understand nothing... > > https://wiki.galaxyproject.org/Admin/Config/UploadviaFTP?action=show&redirect=Admin%2FConfig%2FUpload+via+FTP > > I've configured the universe_wsgi.ini file with > > ftp_upload_dir = galaxy_dist/database/files/ > ftp_upload_site = any adress. > > I use Filezilla to for FTP connecting but it doesn't works and it asks me a > Port ... > Can someone provide to me a simply tutorial to enable ftp upload ? > > Thanks > > Pat > > ___ > 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/
