# 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`.