{"action":"created","issue":{"url":"https://api.github.com/repos/ShahimEssaid/owltools/issues/104","labels_url":"https://api.github.com/repos/ShahimEssaid/owltools/issues/104/labels{/name}","comments_url":"https://api.github.com/repos/ShahimEssaid/owltools/issues/104/comments","events_url":"https://api.github.com/repos/ShahimEssaid/owltools/issues/104/events","html_url":"https://github.com/ShahimEssaid/owltools/issues/104","id":53484193,"number":104,"title":"On Windows with Cygwin, owltools doesn't work in the combination \"Cygwin shell, Windows java\"","user":{"login":"ShahimEssaid","id":4766673,"avatar_url":"https://avatars.githubusercontent.com/u/4766673?v=3","gravatar_id":"","url":"https://api.github.com/users/ShahimEssaid","html_url":"https://github.com/ShahimEssaid","followers_url":"https://api.github.com/users/ShahimEssaid/followers","following_url":"https://api.github.com/users/ShahimEssaid/following{/other_user}","gists_url":"https://api.github.com/users/ShahimEssaid/gists{/gist_id}","starred_url":"https://api.github.com/users/ShahimEssaid/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ShahimEssaid/subscriptions","organizations_url":"https://api.github.com/users/ShahimEssaid/orgs","repos_url":"https://api.github.com/users/ShahimEssaid/repos","events_url":"https://api.github.com/users/ShahimEssaid/events{/privacy}","received_events_url":"https://api.github.com/users/ShahimEssaid/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ShahimEssaid/owltools/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/ShahimEssaid/owltools/labels/imported","name":"imported","color":"FFFFFF"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-01-06T06:01:44Z","updated_at":"2015-01-06T06:02:36Z","closed_at":null,"body":"_From [allegris...@gmail.com](https://code.google.com/u/101450876705855937998/) on October 11, 2014 08:33:45_\n\n\n\\<b>What steps will reproduce the problem?</b>\n&#13;\n1. I have the following shell:&#13;\n&#13;\nGNU bash, version 4.1.17(9)-release-(x86_64-unknown-cygwin)&#13;\n&#13;\n2. I have the following Java:&#13;\n&#13;\njava version \"1.8.0_11\"&#13;\nJava(TM) SE Runtime Environment (build 1.8.0_11-b12)&#13;\nJava HotSpot(TM) 64-Bit Server VM (build 25.11-b03, mixed mode)&#13;\n&#13;\nI downloaded the owltools script and owltools-runner-all.jar.&#13;\n&#13;\nJava, when started from the script, doesn't find the JAR because of path syntax confusion.&#13;\n&#13;\nThe following fixes helped.  Note that I also deleted the setting of java.library.path, as ../lib didn't exist in my environment with the above downloads.&#13;\n&#13;\n--- owltools.orig\t2014-10-11 17:23:24.929368900 +0200&#13;\n+++ owltools\t2014-10-11 17:22:59.057509400 +0200&#13;\n@@ -18,7 +18,12 @@&#13;\n \\# failure message will make a little more sense.&#13;\n \\# JAVAPATH=\"java\"&#13;\n &#13;\n-PATH_SEP=\":\"&#13;\n+if [ \"`uname -o`\" = \"Cygwin\" ]&#13;\n+then&#13;\n+    PATH_SEP=\";\"&#13;\n+else&#13;\n+    PATH_SEP=\":\"&#13;\n+fi&#13;\n &#13;\n JAVAARGS=\" \"&#13;\n CMDARGS=\" \"&#13;\n@@ -27,6 +32,14 @@&#13;\n PATH_TO_ME=`which $0`;&#13;\n PATH_TO_ME=`echo $PATH_TO_ME | sed -e \"s/\\(.*\\)\\/.*/\\1/g\"`&#13;\n &#13;\n+if [ \"`uname -o`\" = \"Cygwin\" ]&#13;\n+then&#13;\n+    LAUNCHER_DIR=\"$PATH_TO_ME\"&#13;\n+else&#13;\n+    LAUNCHER_DIR=\"`cygpath --mixed $PATH_TO_ME`\"&#13;\n+fi&#13;\n+&#13;\n+&#13;\n \\# Just the name of the script.&#13;\n SCRIPTNAME=`echo $PATH_TO_ME | sed -e \"s/.*\\/\\(.*\\)/\\1/g\"`&#13;\n &#13;\n@@ -63,6 +76,10 @@&#13;\n     DEREFERENCED_CLASSPATH=`ls -1 -L $PATH_TO_ME/$ARG | grep -v ontologyrelease`&#13;\n     for CP_ENTRY in $DEREFERENCED_CLASSPATH&#13;\n     do&#13;\n+        if [ \"`uname -o`\" = \"Cygwin\" ]&#13;\n+        then&#13;\n+            CP_ENTRY=\"`cygpath --mixed \\\"$CP_ENTRY\\\"`\"&#13;\n+        fi&#13;\n \tif [ -z \"$CLASSPATH\" ]&#13;\n \tthen&#13;\n \t    CLASSPATH=\"$CP_ENTRY\"&#13;\n@@ -102,7 +119,7 @@&#13;\n fi&#13;\n &#13;\n \\## Assemble and run the final command.&#13;\n-CMD=\"$JAVAPATH -Xms2048M -DentityExpansionLimit=2048000 -Djava.awt.headless=true -Djava.library.path=$PATH_TO_ME/../lib -classpath $CLASSPATH -DlauncherDir=$PATH_TO_ME $JAVAARGS owltools.cli.CommandLineInterface $CMDARGS\"&#13;\n+CMD=\"\\\"$JAVAPATH\\\" -Xms2048M -DentityExpansionLimit=2048000 -Djava.awt.headless=true -classpath \\\"$CLASSPATH\\\" -DlauncherDir=\\\"$LAUNCHER_DIR\\\" $JAVAARGS owltools.cli.CommandLineInterface $CMDARGS\"&#13;\n &#13;\n \\## DEBUG&#13;\n \\## Let's see a little of the environment if we declare DEBUG=1.&#13;\n\n\n\n_Original issue: http://code.google.com/p/owltools/issues/detail?id=104_"},"comment":{"url":"https://api.github.com/repos/ShahimEssaid/owltools/issues/comments/68829838","html_url":"https://github.com/ShahimEssaid/owltools/issues/104#issuecomment-68829838","issue_url":"https://api.github.com/repos/ShahimEssaid/owltools/issues/104","id":68829838,"user":{"login":"ShahimEssaid","id":4766673,"avatar_url":"https://avatars.githubusercontent.com/u/4766673?v=3","gravatar_id":"","url":"https://api.github.com/users/ShahimEssaid","html_url":"https://github.com/ShahimEssaid","followers_url":"https://api.github.com/users/ShahimEssaid/followers","following_url":"https://api.github.com/users/ShahimEssaid/following{/other_user}","gists_url":"https://api.github.com/users/ShahimEssaid/gists{/gist_id}","starred_url":"https://api.github.com/users/ShahimEssaid/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ShahimEssaid/subscriptions","organizations_url":"https://api.github.com/users/ShahimEssaid/orgs","repos_url":"https://api.github.com/users/ShahimEssaid/repos","events_url":"https://api.github.com/users/ShahimEssaid/events{/privacy}","received_events_url":"https://api.github.com/users/ShahimEssaid/received_events","type":"User","site_admin":false},"created_at":"2015-01-06T06:02:36Z","updated_at":"2015-01-06T06:02:36Z","body":"_From [cmung...@gmail.com](https://code.google.com/u/115850439786749293234/) on October 11, 2014 09:09:00_\n\nThis issue was closed by revision r2385 ."}}