diff readme.rst @ 6:3ad7ef0ba385 draft

Use <stdio> because prokka writes some warnings on stderr. Update Orione citation. Update Prokka citation. Support Prokka 1.10. Upgrade dependencies to package_minced_0_1_6, package_barrnap_0_5 and package_tbl2asn_23_7. Added --proteins option. Add <citations>.

--- a/readme.rst	Thu Jan 09 16:49:50 2014 -0500
+++ b/readme.rst	Mon Oct 27 06:45:52 2014 -0400
@@ -4,9 +4,9 @@
 Warning
 -------
 
-Prokka includes custom databases and is thus about a 2.0 GB download!
+Prokka includes custom databases and is thus about a 340 MB download!
 
-Dependencies of Prokka which needs to be installed separately
+Dependencies of Prokka which need to be installed separately
 -------------------------------------------------------------
 
 - Perl core modules: File\::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;
@@ -20,7 +20,7 @@
 Configuration
 -------------
 
-prokka tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see http://wiki.galaxyproject.org/Admin/Config/Jobs and http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ).
+prokka tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see https://wiki.galaxyproject.org/Admin/Config/Jobs and https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ).
 
 If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool.
 
@@ -30,11 +30,12 @@
 
 (where N is the number of CPU cores allocated by the job runner for this tool) to the file
 
-  <tool_dependencies_dir>/prokka/1.7/crs4/prokka/<hash_string>/env.sh
+  <tool_dependencies_dir>/prokka/1.10/crs4/prokka/<hash_string>/env.sh
 
 Version history
 ---------------
 
+- Release 6 (prokka 1.4.0): Use <stdio> because prokka writes some warnings on stderr. Update Orione citation. Update Prokka citation. Support Prokka 1.10. Upgrade dependencies to package_minced_0_1_6, package_barrnap_0_5 and package_tbl2asn_23_7. Added --proteins option. Add <citations>.
 - Release 5 (prokka 1.3.0): Fix Prokka 1.8 dependency installation.
 - Release 4 (prokka 1.3.0): Support Prokka 1.8. Depend on package_minced_0_1_4 and package_tbl2asn_22_4 (requires Galaxy release_2013.11.04 or later). Update citation.
 - Release 3 (prokka 1.2.0): Use $GALAXY_SLOTS instead of $PROKKA_SITE_OPTIONS. Upgrade Barrnap dependency to v. 0.3. Upgrade Infernal dependency to v. 1.1. Depend on package_gnu_parallel_20131122 (requires Galaxy release_2013.11.04 or later).