# 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.

Runtime deps follow the GPhL CentOS8/RHEL8 install doc
(https://www.globalphasing.com/autoproc/manual/installation/CentOS8_64bit/index.html):
CCP4 8.0 and XDS are absolute requirements, ImageMagick is "highly
recommended" for full functionality. All three come in as
`runtime_deps` (`xds/20260616`, `ccp4/8.0`, `ImageMagick/7.1.2-30`) —
the module-load equivalent of the doc's `.bashrc` recipe (source
setup.sh + CCP4 setup + XDS on PATH). The doc's `autoPROC_latest`
symlink trick is not needed: Pmodules versioning covers it.

## Build on Ra

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)

Step 2: load the build tool (modbuild)

```
module use unstable
module load modbuild/2.1.3
```

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>`)

```
modbuild 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).
- `runtime_deps` must reference module versions that exist on Ra: check with
  `module avail xds ccp4 ImageMagick` after an XDS/CCP4 update and adjust.
- ImageMagick/7.1.2-30 is still `unstable`; promote it to stable before promoting
  autoPROC (a stable module may only depend on stable modules).

## Updating runtime_deps without a rebuild

`runtime_deps` land in the generated modulefile, so after editing
`files/config.yaml`:

```
modbuild build --update-modulefiles 20240710
module use MX unstable && module load autoPROC/20240710   # should auto-load xds, ccp4, ImageMagick
```