[galaxy-dev] Blast+ Wrapper: blastdbcmd: range parameter
Hello all, I use the ToolShed NCBI Blast+ Wrappers (https://toolshed.g2.bx.psu.edu/repository?repository_id=1d92ebdf7e8d466c) and I tried to retrieve sequence information from databases. The blastdbcmd comes with the feature to extract a given range of the sequence: -Range string Range of sequence to extract (Format: start-stop) Is this parameter / functionality also part of the wrapper, how can I use this functionality? Thanks, Matthias ___ 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] Galaxy and HTTPS User-authentification
Hi, I have a question regarding the user authentication of Galaxy. As to my knowledge galaxy uses http, also for the authentication, so the User Email and the password are send in clear text. As I like to use Galaxy for user-authentication and due several disadvantages not an external authentification like described here (https://wiki.galaxyproject.org/Admin/Config/ExternalUserDatbases): Is there any way of using https or an encryption-method for sending user email and password. With kind regards, Matthias Enders ___ 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] Installing galaxy with Apache
Hi John, your solution perfectly solved my problem. Thank you! -Ursprüngliche Nachricht- Von: John Chilton [mailto:jmchil...@gmail.com] Gesendet: Friday, June 06, 2014 3:32 PM An: Matthias Enders Cc: galaxy-...@bx.psu.edu Betreff: Re: [galaxy-dev] Installing galaxy with Apache Hmm... sorry for the delay I hope you got this to work. I feel like someone should respond to this but it is difficult to remotely debug web server configuration issues. Should your apache config line: RewriteRule ^(.*) http://localhost:8080$1 [P] be: RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] instead? That is the only guess I have. Thanks for your interest in deploying Galaxy. -John On Mon, Jun 2, 2014 at 7:37 AM, Matthias Enders wrote: > Hi, > > > > this thread is likely related to this one: > > > > http://user.list.galaxyproject.org/Installing-galaxy-with-Apache-td465 > 4499.html > > > > I installed Galaxy on a Ubuntu Server 12.04 system. I followed the > instruction on the link mentioned above and this one: > > https://wiki.galaxyproject.org/Admin/Config/ApacheProxy > > > > Now my issue is: > > > > When I got this configuration in my /etc/apache2/sites-available/default : > > > > RewriteEngine on > > RewriteRule ^/galaxy$ /galaxy/ [R] > > RewriteRule ^/galaxy/static/style/(.*) > /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] > > RewriteRule ^/galaxy/static/scripts/(.*) > /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] > > RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 > [L] > > RewriteRule ^/galaxy/favicon.ico > /home/galaxy/galaxy-dist/static/favicon.ico > [L] > > RewriteRule ^/galaxy/robots.txt > /home/galaxy/galaxy-dist/static/robots.txt > [L] > > RewriteRule ^(.*) http://localhost:8080$1 [P] > > > > Galaxy is visible at www.my_server_url.de but not at > www.my_server_url.de/galaxy > > > > Following the later URL I got this message: > > Proxy Error > > The proxy server received an invalid response from an upstream server. > The proxy server could not handle the request GET /galaxy. > > Reason: DNS lookup failure for: localhost:8080http: > > > Apache/2.2.22 (Ubuntu) Server at www.my_server_url.de Port 80 > > When I change the configuration like this: (make the second line a comment): > > > > RewriteEngine on > > #RewriteRule ^/galaxy$ /galaxy/ [R] > > RewriteRule ^/galaxy/static/style/(.*) > /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] > > RewriteRule ^/galaxy/static/scripts/(.*) > /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] > > RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 > [L] > > RewriteRule ^/galaxy/favicon.ico > /home/galaxy/galaxy-dist/static/favicon.ico > [L] > > RewriteRule ^/galaxy/robots.txt > /home/galaxy/galaxy-dist/static/robots.txt > [L] > > RewriteRule ^(.*) http://localhost:8080$1 [P] > > > > Galaxy is visible both at www.my_server_url.de and at > www.my_server_url.de/galaxy > > > > When I completely remove this part, the “It works!” standard page of > apache is displayed. > > > > The configuration in my universe.ini is as follows: > > host = 127.0.0.1 > > > > [filter:proxy-prefix] > > use = egg:PasteDeploy#prefix > > prefix = /galaxy > > > > [app:main] > > filter-with = proxy-prefix > > cookie_path = /galaxy > > > > Can you please help me with this issue? > > I want to see the “It works!” page at www.my_server_url.de and galaxy > only at www.my_server_urla.de/galaxy. > > > > Thanks in advance! > > > > Kind regards > > Matthias Enders > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this and other > Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Installing galaxy with Apache
Hi, this thread is likely related to this one: http://user.list.galaxyproject.org/Installing-galaxy-with-Apache-td4654499.html I installed Galaxy on a Ubuntu Server 12.04 system. I followed the instruction on the link mentioned above and this one: https://wiki.galaxyproject.org/Admin/Config/ApacheProxy Now my issue is: When I got this configuration in my /etc/apache2/sites-available/default : RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P] Galaxy is visible at www.my_server_url.de<http://www.my_server_url.de> but not at www.my_server_url.de/galaxy<http://www.my_server_url.de/galaxy> Following the later URL I got this message: Proxy Error The proxy server received an invalid response from an upstream server. The proxy server could not handle the request GET /galaxy<http://www.gsa.npz.de/galaxy>. Reason: DNS lookup failure for: localhost:8080http: Apache/2.2.22 (Ubuntu) Server at www.my_server_url.de Port 80 When I change the configuration like this: (make the second line a comment): RewriteEngine on #RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8080$1 [P] Galaxy is visible both at www.my_server_url.de<http://www.my_server_url.de> and at www.my_server_url.de/galaxy<http://www.my_server_url.de/galaxy> When I completely remove this part, the "It works!" standard page of apache is displayed. The configuration in my universe.ini is as follows: host = 127.0.0.1 [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix cookie_path = /galaxy Can you please help me with this issue? I want to see the "It works!" page at www.my_server_url.de<http://www.my_server_url.de> and galaxy only at www.my_server_urla.de/galaxy. Thanks in advance! Kind regards Matthias Enders ___ 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/
