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duan_jandClaude Fable 5 9946b945d1 add autoPROC pmodule

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>

2026-07-17 18:25:29 +02:00

files

add autoPROC pmodule

2026-07-17 18:25:29 +02:00

.licence

added license to autoPROC frome exisiting module 20240710

2025-05-30 10:49:23 +02:00

build

add autoPROC pmodule

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modulefile

add autoPROC pmodule

2026-07-17 18:25:29 +02:00

README.md

add autoPROC pmodule

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README.md

autoPROC

autoPROC (Global Phasing Ltd.) is an automated pipeline for integrating and scaling macromolecular crystallography diffraction data. It is licence-gated: the PSI licence token is committed as autoPROC/.licence and installed into the software tree at build time. CCP4 8.0 and XDS are hard runtime requirements and are pulled in as module dependencies.

Build on Ra

Step 1: login with your -adm account

kinit xxxx_x-adm
aklog

Step 2: load the latest Pmodules package

module use unstable
module load Pmodules/2.0.0

Step 3: stage the licence-gated snapshot. Download it from Global Phasing (needs credentials, so wget in the build script will not work) and save it in this module directory named by its snapshot date. Do NOT commit it (it is proprietary and large; .gitignore already excludes autoPROC_snapshot_*.tar.gz).

cd autoPROC
# e.g. save the download as autoPROC_snapshot_20240710.tar.gz here

Step 4: edit files/config.yaml to add the real snapshot date as the version, and confirm the ccp4 dependency coordinates for this cluster:

module avail ccp4          # adjust ccp4/8.0 in runtime_deps if the name/version differs
vi files/config.yaml

Step 5: build (installs to /opt/psi/MX/autoPROC/<date>)

./build 20240710

Step 6: confirm the module loads and autoPROC is licensed

module use MX unstable
module load autoPROC/20240710
process -h

Assumptions to verify on the first real build

The snapshot tarball has a single top-level directory, so tar --strip-components=1 puts setup.sh directly at $PREFIX/setup.sh. If the layout differs, adjust the strip level in build.
autoPROC reads its licence from the software home, i.e. $autoPROC_home/.licence, which equals $PREFIX/.licence after the strip. build copies .licence there.
If loading the module fails with ... : unbound variable (setup.sh under set -u), add puts stdout "set +x nounset" before the source line in modulefile (same fix used for phenix).
There is no ccp4 module in this repo; runtime_deps references a site CCP4 module. Set the exact name/version from module avail ccp4.