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I'm running the last steps of the testing of the develop version. If it goes all OK, then I'm doing another release. It's a small one this time - but there are some important bug fixes, cf. https://g…
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There's a risk for TIPCC users to use the incorrect pipeline version if they forget to load the 'lg3' module because then `LG3_HOME` is not set and it will default to /home/jocostello/shared/LG3_Pipel…
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Several \*.pbs scripts have PBS declarations that request `bigmem` nodes, e.g.
```sh
#PBS -l nodes=1:bigmem:ppn=12,vmem=200gb
```
Do we really need that? I would think specifying `mem/vmem` would…
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Cool. I just realized that we're now very close in being able to provide a standalone, shared installation of the LG3 Pipeline on the TIPCC cluster and share it via:
```r
$ module load CBC lg3
```
…
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In order to minimize clashes, instead of using:
```sh
SCRATCHDIR=${SCRATCHDIR:-/scratch/${USER:?}}
```
we should use:
```sh
SCRATCHDIR=${SCRATCHDIR:-/scratch/${USER:?}/${PBS_JOBID}}
```
This w…
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It looks like we're soon ready for the next release.
I'm running final tests on Patient157t10 with neither `LG3_OUTPUT_ROOT` nor `LG3_INPUT_ROOT` set. That should complete later tonight (Sunday). …
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Error when submitting, getting "invalid -v syntax" from something in mutdet_submit.sh
I don't see any other output or error files, so this is all I have:
```
[2018-10-24 10:55:44 PDT] BEGIN: ./_run…
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TASKS:
* [x] Run simple ShellCheck test on all scripts
* [x] Add that test on Travis CI
* [x] Fix all ShellCheck warnings/errors
- [x] *.pbs files
- [x] scripts/*.sh files
* [ ] Validate t…
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As part of Ziv Lab needs to run LG3 themselves, I'm going to replace all hard-coded paths in the scripts with environment variables. (I did this back in 2015, but I have to redo it by hand because th…
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