Re: [base] Problems running Tab2Mage Importer, NOT sufficient Disk Space
Jari Häkkinen wrote: Just for your information: Dominic Oyeniran wrote: This is a known issue and has been documented here: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. Please scroll to the usage section right after the installation section. We prefer to use links to the more generic http://baseplugins.thep.lu.se since lev is merely the current host of the baseplugins (and base) and it may changes in the future. That is the above link should be a more archive safe http://baseplugins.thep.lu.se/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt Noted Jari. Thanks. However, I actually got the link from the base website. (At that time I could not remember the website link) This is the flow of what I did: 1. From here: http://base.thep.lu.se/, I clicked on Base plugins website at the Plug-ins section, which takes me to: http://lev.thep.lu.se/trac/baseplugins. 2. Clicking on 'download page' on the plugins site (want to be a downloader?) section takes me to: http://lev.thep.lu.se/trac/baseplugins/wiki/PluginDownload etc .. Hope this is useful a information. Thanks. ¬Dominic - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Problems running Tab2Mage Importer, NOT sufficient Disk Space
I had this problem too, but had not yet got round to figuring out the solution. It is very helpful to read the README.TXT file on the BasePlugins download page before using the tab2mage importer plugin to avoid any issues /problems. The direct link to the file as stated in the last email is : http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. Just an information for other interested users too. Thanks, ¬Dominic Bob MacCallum wrote: Dominic Oyeniran writes: vegard nygaard wrote: I am trying out the Tab2Mage importer. When starting it from the import button in an experiment it quickly returns with an error. I am running it as root on base2.4.3 having added tab2mage importer and Annotation Type and CV Loader as plug-ins. Input file is the genepix example file found at http://www.ebi.ac.uk/~oyeniran/pages/download.html. This is output from the plugin window: Name Run plugin: Tab2Mage Importer Description Priority 4 (1 = highest, 10 = lowest) Status Error: IMPORT FAILS: The directory containing the unzipped files could not be found. You may NOT have sufficient Disk Space Percent complete 100% This is a known issue and has been documented here: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. Please scroll to the usage section right after the installation section. Simply, we recommend not running the importer as the root user. I believe it's advisable to run BASE as an administrator and not the root user as well. In the next release of the importer, a root user will be able to run the importer as well. In my efforts to solve the problem I wanted to inspect the code but was unable to find the java files referred in the stack trace. Where can I find them? In the jar file I found only class files. I downloaded the whole Nutribase-2.0.2-src.zip, but was unable to unpack the file properly. Are the source files for the importer inside and if so how do I unpack the zip file? The source file for the importer is available at: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/src/uk/ - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Problems running Tab2Mage Importer, NOT sufficient Disk Space
And it is also linked from http://lev.thep.lu.se/trac/baseplugins/wiki/uk.ac.ebi.Tab2MageImporter But the readme file is not very precise about this problem, it advices me not to use root. I disregarded that advice :(. If it will only run as a non-root user with a limited quota, that should be stated as an imperative. Changed and checked in. Anyways, I got past that problem now but ran into another one. Error: IMPORT FAILS: The tab2mage file supplied is not compliant with the tab2mage specification I use the genepix example zip file. If this is another known issue please let me know, if not I will look more into it in detail tomorrow and let you know if I am stuck. Please check the exceptions on the server and send it to me to have a look at. ¬Dominic - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Problems running Tab2Mage Importer, NOT sufficient Disk Space
Just for your information: Dominic Oyeniran wrote: This is a known issue and has been documented here: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. Please scroll to the usage section right after the installation section. We prefer to use links to the more generic http://baseplugins.thep.lu.se since lev is merely the current host of the baseplugins (and base) and it may changes in the future. That is the above link should be a more archive safe http://baseplugins.thep.lu.se/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
