Re: [galaxy-dev] (no subject)
HI, Thanks for the reply. actually my server is not connected with the internet. Previously i downloaded in another system with internet connection and installed to server. now i gave internet connection to the server now i could connect to it and download the python eggs. Thanks Sridhar On Sat, May 4, 2013 at 12:36 AM, Adam Brenner aebre...@uci.edu wrote: What version of Python are you using? I believe Python 2.7 is the recommend version. I suggest you grab a fresh copy of galaxy from the stable branch and try again. -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ http://www.ics.uci.edu/%7Eaebrenne/ aebre...@uci.edu On Fri, May 3, 2013 at 12:24 AM, sridhar srinivasan sridhar2bioi...@gmail.com wrote: Dear All, i am installing galaxy first time. i face problem while installing the python eggs. while running the Run.sh command it gives as /home/sbsuser/.python-eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg-tmp/csamtools.so:6: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility � b �n 64 0� c � � � �� ? �� � ��U �#k � ! \ j Z o� [ � � � [ � � �9 - �� ra # ��� �� 8n � �C �U�; B � S l K (p� �� U � � P w 5 ≠ ' H š è π ø * ─ ␋ Ð Ä @ ê i couldn't read the message and also i couldn't open the galaxy page http://localhost:8080 Could you please suggest tth epossibilities to install. Thanks in advance Regards Sridhar ___ 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/
Re: [galaxy-dev] (no subject)
What version of Python are you using? I believe Python 2.7 is the recommend version. I suggest you grab a fresh copy of galaxy from the stable branch and try again. -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu On Fri, May 3, 2013 at 12:24 AM, sridhar srinivasan sridhar2bioi...@gmail.com wrote: Dear All, i am installing galaxy first time. i face problem while installing the python eggs. while running the Run.sh command it gives as /home/sbsuser/.python-eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg-tmp/csamtools.so:6: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility � b �n 64 0� c � � � �� ? �� � ��U �#k � ! \ j Z o� [ � � � [ � � �9 - �� ra # ��� �� 8n � �C �U�; B � S l K (p� �� U � � P w 5 ≠ ' H š è π ø * ─ ␋ Ð Ä @ ê i couldn't read the message and also i couldn't open the galaxy page http://localhost:8080 Could you please suggest tth epossibilities to install. Thanks in advance Regards Sridhar ___ 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/
Re: [galaxy-dev] (no subject)
David, Thank you for reporting this error, which was due to a new tool shed feature being introduced in -central, which had not yet been wrapped in a backwards compatibility layer for -dist. As of 9440:bbb229927c68, the issue should be resolved. --Dave B. On 4/11/13 12:51:03.000, David Bonsall wrote: Dear Galaxy team, I'm trying to install NCBI + tools on a local instance of galaxy (rep: 8.1546099212f), but I get the following error, which I do not get when trying to install other tools. Thank you for all your hard work. It's all much appreciated David Error Traceback: View as: Interactive | Text | XML (full) ⇝ HTTPError: HTTP Error 500: Internal Server Error URL: http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1d92ebdf7e8d466cchangeset_revisions=1f546099212f Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:125 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:182 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:228 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:894 in prepare_for_install view common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) Module tool_shed.util.common_install_util:90 in get_dependencies_for_repository view required_repo_info_dicts = get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) Module tool_shed.util.common_install_util:283 in get_required_repo_info_dicts view response = urllib2.urlopen( url ) Module urllib2:126 in urlopen view return _opener.open(url, data, timeout) Module urllib2:400 in open view response = meth(req, response) Module urllib2:513 in http_response view 'http', request, response, code, msg, hdrs) Module urllib2:438 in error view return self._call_chain(*args) Module urllib2:372 in _call_chain view result = func(*args) Module urllib2:521 in http_error_default view raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error ___ 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/
Re: [galaxy-dev] (no subject)
David, The reason shed_tools should be outside the Galaxy path is that tool shed mercurial repositories can interfere with the Galaxy mercurial repository, since mercurial will find more than one .hg directory. As long as the data you want to store is not a mercurial repository, you should be safe, but my advice would still be to locate it outside the Galaxy path to avoid any possibility of conflicts. --Dave B. On 4/16/13 16:28:01.000, David Bonsall wrote: Thanks Dave A quick update from /galaxy-dist % hg update stable .did the trick! Btw, I have another question I have since added sub-directories to /galaxy-dist to store blast databases etc. Is this bad? Will mercurial be able to update. I remember a warning to not install shed-tools directory in the main galaxy stem for this reason. Does this rule apply to all directories? Best Wishes David On Tue, Apr 16, 2013 at 9:16 PM, Dave Bouvier d...@bx.psu.edu mailto:d...@bx.psu.edu wrote: David, Thank you for reporting this error, which was due to a new tool shed feature being introduced in -central, which had not yet been wrapped in a backwards compatibility layer for -dist. As of 9440:bbb229927c68, the issue should be resolved. --Dave B. On 4/11/13 12:51:03.000, David Bonsall wrote: Dear Galaxy team, I'm trying to install NCBI + tools on a local instance of galaxy (rep: 8.1546099212f), but I get the following error, which I do not get when trying to install other tools. Thank you for all your hard work. It's all much appreciated David Error Traceback: View as: Interactive | Text | XML (full) ⇝ HTTPError: HTTP Error 500: Internal Server Error URL: http://127.0.0.1:8080/admin___toolshed/prepare_for_install?__tool_shed_url=http://toolshed.__g2.bx.psu.edu/repository_ids=__1d92ebdf7e8d466cchangeset___revisions=1f546099212f http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1d92ebdf7e8d466cchangeset_revisions=1f546099212f Module weberror.evalexception.__middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:125 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:182 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:228 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.__controllers.admin_toolshed:894 in prepare_for_install view common_install_util.get___dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) Module tool_shed.util.common_install___util:90 in get_dependencies_for___repository view required_repo_info_dicts = get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) Module tool_shed.util.common_install___util:283 in get_required_repo_info_dicts view response = urllib2.urlopen( url ) Module urllib2:126 in urlopen view return _opener.open(url, data, timeout) Module urllib2:400 in open view response = meth(req, response) Module urllib2:513 in http_response view 'http', request, response, code, msg, hdrs) Module urllib2:438 in error view return self._call_chain(*args) Module urllib2:372 in _call_chain view result = func(*args) Module urllib2:521 in http_error_default view raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error _ 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/ 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:
Re: [galaxy-dev] (no subject)
David, While I look into the cause of this error, could you tell me which revision of Galaxy you're running? --Dave B. On 4/11/13 12:51:03.000, David Bonsall wrote: Dear Galaxy team, I'm trying to install NCBI + tools on a local instance of galaxy (rep: 8.1546099212f), but I get the following error, which I do not get when trying to install other tools. Thank you for all your hard work. It's all much appreciated David Error Traceback: View as: Interactive | Text | XML (full) ⇝ HTTPError: HTTP Error 500: Internal Server Error URL: http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1d92ebdf7e8d466cchangeset_revisions=1f546099212f Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:125 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:182 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:228 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:894 in prepare_for_install view common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) Module tool_shed.util.common_install_util:90 in get_dependencies_for_repository view required_repo_info_dicts = get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) Module tool_shed.util.common_install_util:283 in get_required_repo_info_dicts view response = urllib2.urlopen( url ) Module urllib2:126 in urlopen view return _opener.open(url, data, timeout) Module urllib2:400 in open view response = meth(req, response) Module urllib2:513 in http_response view 'http', request, response, code, msg, hdrs) Module urllib2:438 in error view return self._call_chain(*args) Module urllib2:372 in _call_chain view result = func(*args) Module urllib2:521 in http_error_default view raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error ___ 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/
Re: [galaxy-dev] (no subject)
Security warning: DO NOT CLICK on the link in this thread. Rehan Saleem - it is likely that your original sending hotmail email account has been compromised. We have removed it from the galaxy-...@bx.psu.edu mailing list to prevent further unmoderated posts until the problem is cleared. Contacting your local system administrator for help is one place to start. Anyone who did click on the link already should do the same, as this is usually how such viruses spread, although much depends on OS and other factors. Good luck! Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training 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/
Re: [galaxy-dev] (no subject)
Hello Alfredo, Setting up Galaxy as a production server has many components, so it is difficult to know exactly what the issue may be, especially if you have already followed the instructions on the wiki. For example, if Galaxy just not showing up on your intranet or are you having trouble logging in as non-administrator? Or perhaps you are asking where to look in the wiki? All of these topics are covered in the wiki. This is where to start: http://getgalaxy.org Follow the instructions for 'Advanced Configuration' that begin at the bottom of the primary wiki above, to find this areas: Running Galaxy in a production environment: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server Under the section Using a proxy server find specific instructions for Apache: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy All Administrative resources can be found under: http://wiki.g2.bx.psu.edu/Admin This should help you or your administrator to get things going. If you get stuck at a particular spot, first check to see if it is a network configuration issue local to our site and resolve that as a first step. If it still seems to be a Galaxy configuration issue, then please provide more details. Be sure to keep the galaxy-...@bx.psu.edu mailing list on the cc list - we will want the developer's and community's support in helping to troubleshoot issues. Hopefully this helps, Jen Galaxy team On 10/4/12 8:28 AM, Alfredo Guilherme Silva Souza wrote: Hello everyone. Personnel of aid to put my galaxy that is place to be accessed by other machines already setup apache as the galaxy is on wiki, but I'm not getting access to another computer on my network. Does anyone know how to configure Apache to let the galaxy accessible to other machines? Thank you. -- /*Alfredo Guilherme*/ /* */ ___ 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://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/
Re: [galaxy-dev] (no subject)
Hello Jean! I am using the galaxy in my project CBT (Work Completion of course), I am student of Computer Science. I'll put my project to run on a server of a university to make the presentation, only for this first'm running and configuring everything in my notebook (locally), I followed all the steps to configure apache, just that I can only access the galaxy by the address that I put in the galaxy, if I access my apache can not view the project as configured galaxy. Sorry about my doubts, I think someone may have already gone through it and maybe you can help me. Hugs. 2012/10/4 Jennifer Jackson j...@bx.psu.edu Hello Alfredo, Setting up Galaxy as a production server has many components, so it is difficult to know exactly what the issue may be, especially if you have already followed the instructions on the wiki. For example, if Galaxy just not showing up on your intranet or are you having trouble logging in as non-administrator? Or perhaps you are asking where to look in the wiki? All of these topics are covered in the wiki. This is where to start: http://getgalaxy.org Follow the instructions for 'Advanced Configuration' that begin at the bottom of the primary wiki above, to find this areas: Running Galaxy in a production environment: http://wiki.g2.bx.psu.edu/**Admin/Config/Performance/**Production%20Serverhttp://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server Under the section Using a proxy server find specific instructions for Apache: http://wiki.g2.bx.psu.edu/**Admin/Config/Apache%20Proxyhttp://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy All Administrative resources can be found under: http://wiki.g2.bx.psu.edu/**Admin http://wiki.g2.bx.psu.edu/Admin This should help you or your administrator to get things going. If you get stuck at a particular spot, first check to see if it is a network configuration issue local to our site and resolve that as a first step. If it still seems to be a Galaxy configuration issue, then please provide more details. Be sure to keep the galaxy-...@bx.psu.edu mailing list on the cc list - we will want the developer's and community's support in helping to troubleshoot issues. Hopefully this helps, Jen Galaxy team On 10/4/12 8:28 AM, Alfredo Guilherme Silva Souza wrote: Hello everyone. Personnel of aid to put my galaxy that is place to be accessed by other machines already setup apache as the galaxy is on wiki, but I'm not getting access to another computer on my network. Does anyone know how to configure Apache to let the galaxy accessible to other machines? Thank you. -- /*Alfredo Guilherme*/ /* */ __**_ 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://galaxyproject.org -- *Alfredo Guilherme* * * ___ 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] (no subject)
Hello Susan, Are you still having problem with registration? Please try again, doing the following to register at the Galaxy main public instance. - Start at: http://usegalaxy.org/ - This will take you to: https://main.g2.bx.psu.edu/ - On the top menu, far right, is the User menu. Click on this, there are two options, register is the second. Best, Jen Galaxy team On 6/28/12 1:51 PM, Susan Hester wrote: Hi, I'm trying to register in Galaxy on the public server and under the user tab register is greyed out? How do I register? Susan Hester, Ph.D. Research Biologist Systems Biology Branch Integrated Systems Toxicology Division (ISTD) National Health and Environmental Effects Research Lab US Environmental Protection Agency 109 T.W. Alexander Dr. MD-B143-06 Research Triangle Park, NC 27711 hester.su...@epa.gov ___ 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://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/
Re: [galaxy-dev] (no subject)
Hi Carlos See: galaxy_dist/lib/galaxy/util/__init__.py for characters that are allowed but need to be escaped Regards, Hans On 06/28/2012 03:14 PM, Carlos Reyes wrote: Hello, I have never used this support route before however I have a question about a Galaxy wrapper that I made for a python tool. I have a text input box connected to a $command_line_spot in an attempt to run a string such as IN[4]=='gene' on the command line (quotations included) through text box input. When I put IN[4]=='gene' directly in the command line it runs fine, however when I put it through my text box it puts the string on the command line as __dq__IN__ob__4__cb__==__sq__gene__sqdq__ IN[4]=='gene' instead of just IN[4]=='gene'. Sorry if this email makes no sense whatsoever, it is very out of context but I thought I'd ask. Note: I am running the latest release of galaxy which I pulled from mercurial. Thanks, Carlos The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___ 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/ ___ 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] (no subject)
On 01/24/2012 06:19 AM, Vidya .H.K wrote: Hi, Actually I am not computer expert as well. I have just started to work in this area. so I am not able to figure out how to solve this problem. I request you to elaborate on what you meant in your previous mail. by simulating a complete command line I meant the following: You look how macs_wrapper.py is called by galaxy. This is written in the macs_wrapper.xml and then you execute the same command line. But I just realize, you have re-submitted the same question in a different e-mail thread again (unfortunately, again without a subject line). Thanks in advance As I wrote in my previous e-mail: Please send all follow-up with a cc to the mailing list (reply-all). In order to debug you situation you need to simulate a complete commandline, the same Galaxy is doing. Regards, Hans On 01/23/2012 05:35 AM, Vidya .H.K wrote: Hi, Sorry for delayed reply. When I execute macs_wrapper.py on command line, I get the following error. python macs_wrapper.py File stdin, line 1 python macs_wrapper.py Thanks in advance On 01/10/2012 06:31 AM, Vidya .H.K wrote: Hi, I think macs is exceutable with galaxy user. what happens if you execute macs_wrapper.py on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list (reply-all). On 01/09/2012 05:04 AM, Vidya .H.K wrote: Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged An error occurred running this job: /bin/sh: macs: not found . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans Thanks in advance. Regards vidya ___ 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/ ___ 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] (no subject)
Hi, Actually I am not computer expert as well. I have just started to work in this area. so I am not able to figure out how to solve this problem. I request you to elaborate on what you meant in your previous mail. Thanks in advance As I wrote in my previous e-mail: Please send all follow-up with a cc to the mailing list (reply-all). In order to debug you situation you need to simulate a complete commandline, the same Galaxy is doing. Regards, Hans On 01/23/2012 05:35 AM, Vidya .H.K wrote: Hi, Sorry for delayed reply. When I execute macs_wrapper.py on command line, I get the following error. python macs_wrapper.py File stdin, line 1 python macs_wrapper.py Thanks in advance On 01/10/2012 06:31 AM, Vidya .H.K wrote: Hi, I think macs is exceutable with galaxy user. what happens if you execute macs_wrapper.py on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list (reply-all). On 01/09/2012 05:04 AM, Vidya .H.K wrote: Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged An error occurred running this job: /bin/sh: macs: not found . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans Thanks in advance. Regards vidya ___ 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/ ___ 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] (no subject)
As I wrote in my previous e-mail: Please send all follow-up with a cc to the mailing list (reply-all). In order to debug you situation you need to simulate a complete commandline, the same Galaxy is doing. Regards, Hans On 01/23/2012 05:35 AM, Vidya .H.K wrote: Hi, Sorry for delayed reply. When I execute macs_wrapper.py on command line, I get the following error. python macs_wrapper.py File stdin, line 1 python macs_wrapper.py Thanks in advance On 01/10/2012 06:31 AM, Vidya .H.K wrote: Hi, I think macs is exceutable with galaxy user. what happens if you execute macs_wrapper.py on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list (reply-all). On 01/09/2012 05:04 AM, Vidya .H.K wrote: Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged An error occurred running this job: /bin/sh: macs: not found . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans Thanks in advance. Regards vidya ___ 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/ Regards H.K.VIDYA - Institute of Bioinformatics and Applied Biotechnology, Bangalore ___ 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] (no subject)
On 01/10/2012 06:31 AM, Vidya .H.K wrote: Hi, I think macs is exceutable with galaxy user. what happens if you execute macs_wrapper.py on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list (reply-all). On 01/09/2012 05:04 AM, Vidya .H.K wrote: Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged An error occurred running this job: /bin/sh: macs: not found . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans Thanks in advance. Regards vidya ___ 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/ Regards H.K.VIDYA PGDB-10-10-33 - Institute of Bioinformatics and Applied Biotechnology, Bangalore ___ 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] (no subject)
On 01/09/2012 05:04 AM, Vidya .H.K wrote: Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged An error occurred running this job: /bin/sh: macs: not found . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans Thanks in advance. Regards vidya ___ 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/ ___ 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] (no subject)
Kristen Eisenberg wrote: [galaxy-dev] Failure to prepare job error Hello, I'm running a Python/R tool from my Amazon Galaxy instance. To use R, I import a package I've installed called PypeR. My tool works fine from the command line, but when I try to run it on my Amazon instance, it gives me this error: Traceback (most recent call last): File /nfs/software/galaxy/lib/galaxy/jobs/runners/local.py, line 61, in run_job job_wrapper.prepare() File /nfs/software/galaxy/lib/galaxy/jobs/__init__.py, line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /nfs/software/galaxy/lib/galaxy/tools/__init__.py, line 1543, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /nfs/software/galaxy/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /nfs/software/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-i686-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File cheetah_DynamicallyCompiledCheetahTemplate_1311891781_86_41894.py, line 83, in respond EOFError: EOF when reading a line With the additional caption failure to prepare job. I've been struggling with this for days, and I'm pretty sure I don't have a typo in my .xml file. How can I solve this? Hi Kristen, Could you post the relevant XML file to the list? The error unfortunately indicates a syntax error or typo. --nate Kristen Eisenberg Billige Flüge Marketing GmbH Emanuelstr. 3, 10317 Berlin Deutschland Telefon: +49 (33) 5310967 Email: utebachmeier at gmail.com Site: http://flug.airego.de - Billige Flüge vergleichen ___ 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/ ___ 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/
