0fe06c81066186e06a5cd7a82d12839928ae23f2
capsules.md
... | ... | @@ -1,6 +1,6 @@ |
1 | 1 | # SBGrid software environment |
2 | 2 | |
3 | -The SBGrid Capsule software environment which is significantly faster than the older 'monolithic' shell environment. This environment includes added features for users to manage software versions and duplicate executables. Older features (such as version selection) are still present but improved. Old scripts should run unaltered and no new commands are required. |
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3 | +The SBGrid Capsule software environment includes features for users to manage software versions and duplicate executables. Older features (such as version selection) are still present but improved. Old scripts should run unaltered and no new commands are required. |
|
4 | 4 | |
5 | 5 | - [SBGrid software environment](#sbgrid-software-environment) |
6 | 6 | - [Notable features of Capsules](#notable-features-of-capsules) |
... | ... | @@ -84,14 +84,14 @@ Setting the version - EXAMPLE |
84 | 84 | For the refine executable, the default version show here is 20160324. |
85 | 85 | |
86 | 86 | ``` |
87 | - bash-4.1$ refine --sbwhich |
|
87 | + $ refine --sbwhich |
|
88 | 88 | /programs/x86_64-linux/buster/20160324/autoBUSTER/bin/linux64/refine |
89 | 89 | ``` |
90 | 90 | |
91 | 91 | We can change this by setting the variable BUSTER_X to 20151214 and calling sbwhich in one command : |
92 | 92 | |
93 | 93 | ``` |
94 | - bash-4.1$ env BUSTER_X=20151214 refine --sbwhich |
|
94 | + $ env BUSTER_X=20151214 refine --sbwhich |
|
95 | 95 | /programs/x86_64-linux/buster/20151214/autoBUSTER/bin/linux64/refine |
96 | 96 | ``` |
97 | 97 | |
... | ... | @@ -130,39 +130,39 @@ Sometimes a duplicate occurs with an executable that is outside of the SBGrid or |
130 | 130 | |
131 | 131 | Which executable am I using? |
132 | 132 | |
133 | - -bash-4.1 refine --sbwhich |
|
133 | + $ refine --sbwhich |
|
134 | 134 | /programs/x86_64-linux/buster/20160324/autoBUSTER/bin/linux64/refine |
135 | 135 | |
136 | 136 | What packages include this executable? |
137 | 137 | |
138 | - -bash-4.1$ refine --sbapp:l |
|
138 | + $ refine --sbapp:l |
|
139 | 139 | buster |
140 | 140 | eman |
141 | 141 | |
142 | 142 | refine is present in buster and eman. Where is the eman executable? |
143 | 143 | |
144 | - -bash-4.1$ refine --sbapp:a eman --sbwhich |
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144 | + $ refine --sbapp:a eman --sbwhich |
|
145 | 145 | /programs/x86_64-linux/eman/1.9/bin/refine |
146 | 146 | |
147 | 147 | or |
148 | 148 | |
149 | 149 | ``` |
150 | - -bash-4.1$ env _REFINE=eman refine --sbwhich |
|
150 | + $ env _REFINE=eman refine --sbwhich |
|
151 | 151 | /programs/x86_64-linux/eman/1.9/bin/refine |
152 | 152 | ``` |
153 | 153 | |
154 | 154 | I'd like set the eman refine as my default version |
155 | 155 | |
156 | - -bash-4.1$ echo eman > ~/.sbgrid_capsule/refine |
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156 | + $ echo eman > ~/.sbgrid_capsule/refine |
|
157 | 157 | |
158 | 158 | Verify that is the case |
159 | 159 | |
160 | - -bash-4.1$ refine --sbwhich |
|
160 | + $ refine --sbwhich |
|
161 | 161 | /programs/x86_64-linux/eman/1.9/bin/refine |
162 | 162 | |
163 | 163 | List all 'refine' executables and select ( and run ) the version from buster |
164 | 164 | |
165 | - -bash-4.1$ refine --sbapp:s |
|
165 | + $ refine --sbapp:s |
|
166 | 166 | 1) buster |
167 | 167 | 2) eman |
168 | 168 | 3) Cancel |
... | ... | @@ -172,24 +172,24 @@ List all 'refine' executables and select ( and run ) the version from buster |
172 | 172 | List all applications that provide xterm, select userpath, make it my default |
173 | 173 | |
174 | 174 | ``` |
175 | - -bash-4.1$ xterm --sbwhich |
|
175 | + $ xterm --sbwhich |
|
176 | 176 | /programs/x86_64-linux/system/xterm/327/bin/xterm |
177 | 177 | |
178 | - -bash-4.1$ xterm --sbapp:l |
|
178 | + $ xterm --sbapp:l |
|
179 | 179 | xterm |
180 | 180 | /usr/bin/xterm |
181 | 181 | |
182 | - -bash-4.1$ env _XTERM=userpath xterm --sbwhich |
|
182 | + $ env _XTERM=userpath xterm --sbwhich |
|
183 | 183 | /usr/bin/xterm |
184 | 184 | |
185 | - -bash-4.1$ xterm --sbapp:s --sbwhich |
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185 | + $ xterm --sbapp:s --sbwhich |
|
186 | 186 | 1) xterm |
187 | 187 | 2) userpath |
188 | 188 | 3) Cancel |
189 | 189 | Please select application 2 |
190 | 190 | /usr/bin/xterm |
191 | 191 | |
192 | - -bash-4.1$ echo userpath > ~/.sbgrid_capsule/xterm |
|
192 | + $ echo userpath > ~/.sbgrid_capsule/xterm |
|
193 | 193 | ``` |
194 | 194 | |
195 | 195 | Please report any bugs to bugs@sbgrid.org |