duan_jandClaude Fable 5
9946b945d1
Scaffold the standard 4-file Pmodule for autoPROC (Global Phasing Ltd.): build, modulefile, files/config.yaml, README.md. The PSI licence token (autoPROC/.licence) already existed and is installed into the software tree at build time. Follows the phenix archetype for the licence-gated install: the snapshot tarball cannot be wget'd (download needs credentials), so it is staged by hand in the module dir as autoPROC_snapshot_<date>.tar.gz and unpacked into PREFIX with --strip-components=1 (xds pattern). Runtime is activated by sourcing setup.sh via the modulefile. CCP4 8.0 and XDS are wired as runtime_deps (xds from this repo; ccp4 is a site module placeholder to confirm with `module avail ccp4`). Adds a .gitignore guard so the proprietary snapshot is never committed. Not built locally - to be tested on Ra. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
69 lines
2.1 KiB
Markdown
69 lines
2.1 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: login with your `-adm` account
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```
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kinit xxxx_x-adm
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aklog
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```
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Step 2: load the latest Pmodules package
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```
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module use unstable
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module load Pmodules/2.0.0
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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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./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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