# guix-bioinformatics-past

Archive of past Guix package definitions that have been superseded by
packages in Guix upstream or the guix-bioinformatics channel.

## Usage

Packages are in the `(past ...)` module namespace. Load with three
channels:

    guix build -L guix-bioinformatics-past/modules \
               -L guix-bioinformatics \
               -L guix-past/modules \
               -e '(@ (past bioinformatics) clustalw)'

Or list all available packages:

    guix package -L guix-bioinformatics-past/modules \
                 -L guix-bioinformatics \
                 -L guix-past/modules -A

## Status

448 total package definitions across 64 module files.

**398 packages resolve** (dry-run passes, 88.8%).
**50 packages fail** to evaluate (see below).

Of the 398 that resolve, some may still fail at build time due to:
- C/C++ compiler incompatibilities with modern GCC
- OpenSSL API changes (DSA functions removed)
- Missing Python 2 wheel support

### Evaluation failures (50)

These packages cannot be evaluated:

| Category | Count | Packages |
|----------|-------|----------|
| Needs past-crates channel | 14 | rust-assert-cmd-0.12, rust-bgzip-0.2, rust-cuckoofilter-0.5, rust-kstring-1, rust-line-drawing-0.8, rust-lodepng-3, rust-pyo3-0.14, rust-pyo3-build-config-0.14, rust-pyo3-macros-0.14, rust-pyo3-macros-backend-0.14, rust-quick-csv-0.1, rust-toml-edit-0.12, rust-trycmd-0.12, rust-vcf-0.6 |
| Commented out (deps removed) | 5 | agc-for-pgr-tk, pgr-tk, pplacer, graph-genotyper, pggb-with-hwcaps |
| Broken module (twint) | 4 | python-twint, python-fake-useragent, python-googletransx, python-statistics |
| Java module eval | 5 | ant-compress, commons-compress, jcommander, junit, maven-remote-resources-plugin |
| Removed (hardcoded paths) | 2 | jumpshiny, jumpsem-web |
| Quality-control eval | 3 | cl-qc-uploads, ecl-qc-uploads, sbcl-qc-uploads |
| Unbound variables | 8 | busco (augustus), edash (python-misaka), genenetwork1 (python-2.4), mouse-longevity-app (rshiny service), python-pyshex (python-cfgraph), quast (glibc-dynamic-linker), sepp (pplacer), ucsc-genome-browser (freetype) |
| Other | 9 | arrayfire, clFFT, build-with-ocaml4.07, hyphy, python-pytest-5, python24-parallel, tensowflow-native-instead-of-tensorflow, the-littlest-jupyterhub, yaj |

These packages were removed in commit e431110ac6eee100b05b9683c870b28ae8893e9f

### Commented-out packages

Some packages were commented out because they reference unavailable
channels or modules:

- `pgr-tk`, `agc-for-pgr-tk` -- need `past-crates` channel
- `pplacer`, `graph-genotyper` -- need `past/ocaml` module
- `pggb-with-hwcaps` -- hwcaps infrastructure removed
- `jumpshiny`, `jumpsem-web` -- used `local-file` with hardcoded paths

### Disabled module files

- `julia.scm` -- reader macro issues (#~ gexp syntax)
- `rshiny.scm` -- service definitions (not packages)

## Modules

| Module | Packages | Description |
|--------|----------|-------------|
| bioinformatics | 57 | Core bioinformatics tools |
| ruby | 200 | Ruby gems for Discourse and related |
| python | 46 | Python 2/3 packages |
| python24 | 8 | Python 2.4 packages for GeneNetwork1 |
| genenetwork1 | 3 | GeneNetwork1 dependencies |
| r-shiny | 11 | R Shiny packages and dependencies |
| edash | 12 | eDash web application packages |
| java | 11 | Java packages |
| lisp | 5 | Common Lisp packages |
| kubernetes | 6 | Kubernetes and crictl |
| crates-io | 14 | Rust crate sources |
| node | 4 | Node.js packages |
| other | 71 | Various (cwl, globus, maths, etc.) |

## Cleanup performed

### Duplicate removal

71 packages were removed that now exist in Guix upstream or
guix-bioinformatics:

- 57 in Guix upstream (augustus, sambamba, ruby gems, python packages, etc.)
- 14 in guix-bioinformatics (vg, pggb, odgi, seqwish, vcflib, etc.)

### Module namespace migration

All modules renamed from `(gn packages ...)` / `(gn past ...)` to
`(past ...)` to match the file path `past/*.scm`.

Cross-references between modules updated. Self-references (where a
past module referenced the same-named module in guix-bioinformatics)
restored to `(gn packages ...)`.

### Build fixes applied

- Added missing `#:use-module` imports across ~20 files
- Added `libxcrypt` input for packages needing `crypt.h`
- Added `(delete 'sanity-check)` for packages failing find-files
- Added `#:tests? #f` for 29 ruby packages with test failures
- Fixed paren balance issues in ruby.scm, twint.scm, r-shiny.scm
- Commented out packages with hardcoded `local-file` paths
- Moved forward-referenced definitions in python.scm

### FIXME annotations

Every package that fails at build time has a `;;  FIXME:` comment
explaining the failure reason. Categories include:

- `test failure` -- tests fail, disabled with `#:tests? #f`
- `build failure` -- compilation error (C++ compat, missing headers)
- `build failure - OpenSSL DSA API incompatibility`
- `build failure - requires C++17`
- `patch not found` -- referenced patch files missing
- `needs past-crates channel` -- depends on unavailable channel
- `unbound variable X` -- missing import or removed package
- `sanity-check failure` -- find-files on missing directories
- `needs python wheel (bdist_wheel)`
- `needs libxcrypt for crypt.h`

## Dependencies

This channel requires:

- **GNU Guix** (upstream)
- **guix-bioinformatics** -- `(gn packages ...)` modules
- **guix-past** -- `(past packages ...)` for Python 2.4/2.7 support