Creating Maps on SmallWorld: Difference between revisions
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===Step 1: Create the /sw directory=== | ===Step 1: Create the /sw directory=== | ||
SmallWorld requires a /sw directory which contains /anon and /maps | SmallWorld requires a /sw directory which contains /anon and /maps | ||
The /sw directory is located on n-9-22 in /srv/db4 | The /sw directory is located on n-9-22 in | ||
/srv/db4 | |||
This directory contains: | This directory contains: | ||
The /anon directory contains pre-computed subgraphs | The /anon directory contains pre-computed subgraphs | ||
The /maps directory contains text files computed by SmallWorld that map your molecules of choice to the corresponding nodes in the anonymous graph index | The /maps directory contains text files computed by SmallWorld that map your molecules of choice to the corresponding nodes in the anonymous graph index | ||
===Step 2: Find a location for the sw.jar file=== | ===Step 2: Find a location for the sw.jar file=== | ||
Revision as of 19:23, 10 April 2019
Written by Jennifer Young on April 10, 2019
Install
Step 1: Create the /sw directory
SmallWorld requires a /sw directory which contains /anon and /maps The /sw directory is located on n-9-22 in
/srv/db4
This directory contains: The /anon directory contains pre-computed subgraphs The /maps directory contains text files computed by SmallWorld that map your molecules of choice to the corresponding nodes in the anonymous graph index
Step 2: Find a location for the sw.jar file
Copy the sw.jar file to a reasonable location such as
/opt/nextmove/sw.jar
Run
Important! Currently, we only run SmallWorld map generation on n-9-22
Step 1: Set SWDIR environment variable
Determine where the /sw directory with the /anon and /maps directory and if using csh, set the SWDIR variable using
setenv SWDIR /srv/db4
If using bash, set the SWDIR variable using
export SWDIR=/srv/db4
Step 2: Generate the map files
Run sw.jar to convert your smiles file into a map file.
(Optional: use the time command to see how long this takes)
(Optional: tee your results into a log file to check progress)
Here is an example where wait-ok.smi is your .smi file to map:
(time java -jar /opt/nextmove/sw.jar map /mnt/nfs/ex9/work/smallworld/wait-ok.smi
-T /mnt/nfs/ex9/work/smallworld/scratch_sw
-o /mnt/nfs/ex9/work/smallworld/wait-ok.anon.map
-u /mnt/nfs/ex9/work/smallworld/wait-ok.anon.unmapped)
|& tee /mnt/nfs/ex9/work/smallworld/wait-ok_log
For now, generate the map files in the /mnt/nfs/ex9/work/smallworld directory so they can be easily moved to the maps directory when the server is restarted