capsules.md
... ...
@@ -6,6 +6,7 @@
6 6
- [Usage - Capsule Environment for SBGrid](#usage-capsule-environment-for-sbgrid)
7 7
- [Overrides - managing versions :](#usage-capsule-environment-for-sbgrid_overrides-managing-versions)
8 8
- [Managing Duplicate executables](#usage-capsule-environment-for-sbgrid_managing-duplicate-executables)
9
+ - [Managing Duplicate with userpath](#usage-capsule-environment-for-sbgrid_managing-duplicate-userpath)
9 10
- [EXAMPLES:](#usage-capsule-environment-for-sbgrid_examples)
10 11
11 12
<a name="overview"></a>
... ...
@@ -102,15 +103,30 @@ In some cases an executable may exist in multiple applications, i.e. the program
102 103
103 104
You can override the default in 4 ways. They are
104 105
105
-1. Command Line arguments selct the application for a single command :
106
+1. Command Line arguments select the application for a single command :
106 107
**--sbapp:a <appname>** runs the executable from "appname" or
107 108
**--sbapp:s** select application from a list
108 109
109
-2. Environment variable of the form ```_<APPLICATION>```, an underscore followed by executable in UPPER CASE. e.g. ```_XIA2=dials``` will use xia2 executable from "dials".
110
+2. Environment variable of the form ```_<EXECUTABLE>```, an underscore followed by executable in UPPER CASE. e.g. ```_XIA2=dials``` will use xia2 executable from "dials".
110 111
111 112
3. A User Config_file in *~/.sbgrid_capsule/<execname>*. e.g. echo dials > ~/.sbgrid_capsules/xia2 will uset the shell to always use the xia2 from "dials"
112 113
113
-4. A localsite file in */programs/local/capsule/${SB_ARCH}/defaults/execname*
114
+4. A localsite file in *${SB_BASE}/local/capsule/${SB_ARCH}/defaults/execname*
115
+
116
+<a name="usage-capsule-environment-for-sbgrid_managing-duplicate-userpath"></a>
117
+### Managing Duplicate with userpath
118
+
119
+Sometimes a duplicate occurs with an executable that is outside of the SBGrid or BioGrids software tree. For example xterm on x86_64-linux is provided by sbgrid and usually provided by the operating system. A user may use the "userpath" directive to select the one that is accessible from the PATH prior to sourcing the SBGrid/BioGrids environment.
120
+
121
+1. Command Line arguments select the application for a single command :
122
+ **--sbapp:s** select application from a list
123
+
124
+2. Environment variable of the form ```_<EXECUTABLE>```, an underscore followed by executable in UPPER CASE. e.g. ```_XTERM=userpath``` will use xterm fromt he user's original path.
125
+
126
+3. A User Config_file in *~/.sbgrid_capsule/<execname>*. e.g. ```echo userpath > ~/.sbgrid_capsules/xterm ``` will set the SBGrid/BioGrids shells to alwasy use the user's path.
127
+
128
+4. A localsite file in *${SB_BASE}/local/capsule/${SB_ARCH}/defaults/execname*
129
+
114 130
115 131
<a name="usage-capsule-environment-for-sbgrid_examples"></a>
116 132
### EXAMPLES:
... ...
@@ -154,4 +170,27 @@ List all 'refine' executables and select ( and run ) the version from buster
154 170
/programs/x86_64-linux/buster/20160324/autoBUSTER/bin/linux64/refine
155 171
156 172
173
+List all applications that provide xterm, select userpath, make it my default
174
+```
175
+ -bash-4.1$ xterm --sbwhich
176
+ /programs/x86_64-linux/system/xterm/327/bin/xterm
177
+
178
+ -bash-4.1$ xterm --sbapp:l
179
+ xterm
180
+ /usr/bin/xterm
181
+
182
+ -bash-4.1$ env _XTERM=userpath xterm --sbwhich
183
+ /usr/bin/xterm
184
+
185
+ -bash-4.1$ xterm --sbapp:s --sbwhich
186
+ 1) xterm
187
+ 2) userpath
188
+ 3) Cancel
189
+ Please select application 2
190
+ /usr/bin/xterm
191
+
192
+ -bash-4.1$ echo uerpath > ~/.sbgrid_capsules/xterm
193
+```
194
+
157 195
Please report any bugs to bugs@sbgrid.org
196
+