duan_jandClaude Fable 5
c3c38856b3
Main README: clone/SSH/branching quickstart with full /das paths, --tmpdir/--distdir as part of the standard build command (do not fill /var/tmp or $HOME) with cleanup for defaults, tips deduplicated against module READMEs, old-system references removed, resource links and tutorial acknowledgements added. Module READMEs: purge outdated recipes repo-wide — Pmodules/1.1.20 and 2.0.0 plus ./build replaced by modbuild/2.1.3 invocations; the cctbx unbound-variable fix moved from the main README into phenix and DIALS READMEs where it belongs. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
64 lines
2.3 KiB
Markdown
64 lines
2.3 KiB
Markdown
# autoPROC
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autoPROC (Global Phasing Ltd.) is an automated pipeline for integrating and scaling
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macromolecular crystallography diffraction data. It is licence-gated: the PSI licence
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token is committed as `autoPROC/.licence` and installed into the software tree at build
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time. CCP4 8.0 and XDS are hard runtime requirements and are pulled in as module
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dependencies.
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## Build on Ra
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Step 1: make sure you are in the `unx-mx_adm` group -- no -adm account needed, members can update the modules in `/opt/psi/MX` directly (if you have problems, please let the admins know)
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Step 2: load the build tool (modbuild)
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```
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module use unstable
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module load modbuild/2.1.3
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```
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Step 3: stage the licence-gated snapshot. Download it from Global Phasing (needs
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credentials, so `wget` in the build script will not work) and save it in this module
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directory named by its snapshot date. Do NOT commit it (it is proprietary and large;
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`.gitignore` already excludes `autoPROC_snapshot_*.tar.gz`).
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```
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cd autoPROC
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# e.g. save the download as autoPROC_snapshot_20240710.tar.gz here
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```
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Step 4: edit `files/config.yaml` to add the real snapshot date as the version, and
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confirm the `ccp4` dependency coordinates for this cluster:
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```
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module avail ccp4 # adjust ccp4/8.0 in runtime_deps if the name/version differs
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vi files/config.yaml
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```
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Step 5: build (installs to `/opt/psi/MX/autoPROC/<date>`)
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```
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modbuild build 20240710
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```
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Step 6: confirm the module loads and autoPROC is licensed
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```
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module use MX unstable
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module load autoPROC/20240710
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process -h
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```
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## Assumptions to verify on the first real build
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- The snapshot tarball has a single top-level directory, so `tar --strip-components=1`
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puts `setup.sh` directly at `$PREFIX/setup.sh`. If the layout differs, adjust the
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strip level in `build`.
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- autoPROC reads its licence from the software home, i.e. `$autoPROC_home/.licence`,
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which equals `$PREFIX/.licence` after the strip. `build` copies `.licence` there.
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- If loading the module fails with `... : unbound variable` (setup.sh under `set -u`),
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add `puts stdout "set +x nounset"` before the `source` line in `modulefile` (same fix
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used for phenix).
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- There is no `ccp4` module in this repo; `runtime_deps` references a site CCP4 module.
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Set the exact name/version from `module avail ccp4`.
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