Make these pangenome packages tunable

2 files changed, 20 insertions, 0 deletions

diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm
index 817fc65..3e9d8cc 100644
--- a/gn/packages/pangenome-rust.scm
+++ b/gn/packages/pangenome-rust.scm
@@ -3290,6 +3290,7 @@
       (arguments (list #:install-source? #f))
       ;; No upstream test data; tests require GFA/BAM input files.
       (inputs (cargo-inputs 'gfainject #:module '(gn packages pangenome-rust)))
+      (properties '((tunable? . #t)))
       (home-page "https://github.com/pangenome/gfainject")
       (synopsis "Map BAM alignments to GFA graph paths as GAF records")
       (description
@@ -3317,6 +3318,7 @@ names must match the path names in the GFA.")
       (arguments
        (list #:install-source? #f))
       (inputs (cargo-inputs 'onecode #:module '(gn packages pangenome-rust)))
+      (properties '((tunable? . #t)))
       (home-page "https://github.com/pangenome/onecode-rs")
       (synopsis "Rust bindings for ONEcode genomic data format")
       (description
@@ -3351,6 +3353,7 @@ data.  The C library (ONElib) is bundled and compiled at build time.")
              #:cargo-build-flags ''("--release" "--package" "ragc-cli")
              ;; Workspace root has no [[bin]], must specify the CLI member
              #:cargo-install-paths ''("ragc-cli")))
+      (properties '((tunable? . #t)))
       (home-page "https://github.com/AndreaGuarracino/ragc")
       (synopsis "Genome compression tool implementing the AGC format in Rust")
       (description
@@ -3409,6 +3412,7 @@ similar genome sequences and is compatible with the C++ AGC format.")
                    (lambda _
                      (substitute* "guix-vendor/rust-home-0.5.12.tar.gz/Cargo.toml"
                        (("rust-version = \"[^\"]*\"\n") "")))))))
+      (properties '((tunable? . #t)))
       (home-page "https://github.com/pangenome/fastga-rs")
       (synopsis "Rust bindings for FastGA genome aligner with extended CIGAR support")
       (description
@@ -3492,6 +3496,7 @@ alignment (POA) algorithm used to generate consensus sequences.  It supports
 local, global and semi-global alignment modes with linear, affine and convex
 gap modes.")
       (license license:expat)
+      (properties '((tunable? . #t)))
       (home-page "https://github.com/rvaser/spoa"))))
 
 ;;;
@@ -3785,6 +3790,7 @@ sequences to accelerate the alignment process.")
                      zlib
                      (list zstd "lib")
                      (cargo-inputs 'impg #:module '(gn packages pangenome-rust))))
+      (properties '((tunable? . #t)))
       (home-page "https://github.com/pangenome/impg")
       (synopsis "Tool to extract and compute graphs of sequences and alignments")
       (description "IMplicit Pangenome Graph (impg) is a tool that takes in
@@ -3810,6 +3816,7 @@ and alignments for analysis.  It can also compute graphs for the sequences.")
       (build-system cargo-build-system)
       (arguments (list #:install-source? #f))
       (inputs (cargo-inputs 'gfautil #:module '(gn packages pangenome-rust)))
+      (properties '((tunable? . #t)))
       (home-page "https://github.com/pangenome/rs-gfa-utils")
       (synopsis "Command line tools for working with GFA files")
       (description
@@ -3835,6 +3842,7 @@ Graphical Fragment Assembly} files and related formats.")
      `(#:install-source? #f))
     (inputs (cargo-inputs 'gfaffix
                           #:module '(gn packages pangenome-rust)))
+    (properties '((tunable? . #t)))
     (home-page "https://github.com/marschall-lab/GFAffix")
     (synopsis "Identify walk-preserving shared affixes in variation graphs")
     (description
@@ -3859,6 +3867,7 @@ collapses them into a non-redundant graph structure.")
       (build-system cargo-build-system)
       (arguments (list #:install-source? #f))
       (inputs (cargo-inputs 'gafpack #:module '(gn packages pangenome-rust)))
+      (properties '((tunable? . #t)))
       (home-page "https://github.com/ekg/gafpack")
       (synopsis "Convert variation graph alignments to coverage maps over nodes")
       (description
@@ -3883,6 +3892,7 @@ maps useful in haplotype-based genotyping.")
     (build-system cargo-build-system)
     (arguments (list #:install-source? #f))
     (inputs (cargo-inputs 'vcfbub #:module '(gn packages pangenome-rust)))
+    (properties '((tunable? . #t)))
     (home-page "https://github.com/pangenome/vcfbub")
     (synopsis "Popping bubbles in vg deconstruct VCFs")
     (description "vcfbub filters VCF records by snarl tree level and allele
diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
index 1a4d6af..b605fd1 100644
--- a/gn/packages/pangenome.scm
+++ b/gn/packages/pangenome.scm
@@ -86,6 +86,7 @@
                                (append
                                 (find-files "include" "\\.h$")
                                 (find-files "safeclib" "^safe_.*\\.h$"))))))))
+      (properties '((tunable? . #t)))
       (home-page "https://github.com/intel/safestringlib")
       (synopsis "Intel Safe String Library")
       (description
@@ -151,6 +152,7 @@ perform bounds checking and return meaningful error codes.")
     ;; xeonbsw) require a BWA-MEM2 genome index and reads; no standalone
     ;; test data is shipped upstream.
     (supported-systems '("x86_64-linux"))
+    (properties '((tunable? . #t)))
     (home-page "https://github.com/bwa-mem2/bwa-mem2")
     (synopsis "Next generation of the BWA-MEM short read aligner")
     (description
@@ -196,6 +198,7 @@ with a runtime dispatcher.")
                    (install-file "miniprot.1"
                                  (string-append #$output "/share/man/man1")))))))
     (inputs (list zlib))
+    (properties '((tunable? . #t)))
     (home-page "https://github.com/lh3/miniprot")
     (synopsis "Protein-to-genome aligner")
     (description
@@ -237,6 +240,7 @@ protein-coding genes in a new genome using related genomes as references.")
                    (install-file "pangene.1"
                                  (string-append #$output "/share/man/man1")))))))
     (inputs (list zlib))
+    (properties '((tunable? . #t)))
     (home-page "https://github.com/lh3/pangene")
     (synopsis "Construct pangenome gene graphs")
     (description
@@ -296,6 +300,7 @@ suitable for downstream pangenome analysis.")
                      (("export PKG_CONFIG_PATH=\\$\\{PWD\\}/src/ocv/lib/pkgconfig/:\\$\\{PWD\\}/src/ocv/lib64/pkgconfig/:\\$\\{PKG_CONFIG_PATH\\} && ")
                       "")))))))
     ;; No upstream test suite; the tool requires BAM/CRAM input files.
+    (properties '((tunable? . #t)))
     (home-page "https://github.com/tobiasrausch/wally")
     (synopsis "Read alignment visualization tool")
     (description
@@ -338,6 +343,7 @@ and heatmaps for structural variant and genome assembly analysis.")
                      (for-each (lambda (f)
                                  (install-file f bin))
                                (find-files "../build/bin" "."))))))))
+    (properties '((tunable? . #t)))
     (home-page "https://github.com/marbl/meryl")
     (synopsis "Genomic k-mer counter and set operations")
     (description
@@ -369,6 +375,7 @@ difference) on k-mer databases.")
              #:install-source? #f))
       (inputs (list go-github-com-spf13-cobra
                     go-github-com-cheggaaa-pb-v3))
+      (properties '((tunable? . #t)))
       (home-page "https://github.com/davidebolo1993/kfilt")
       (synopsis "K-mer based sequence filtering tool")
       (description
@@ -427,6 +434,7 @@ unmapped reads using unique k-mers from pangenome graph alleles.")
              samtools
              snakemake
              util-linux))
+      (properties '((tunable? . #t)))
       (home-page "https://github.com/pjotrp/cosigt")
     (synopsis "Cosine similarity-based structural haplotype genotyper")
     (description
@@ -485,6 +493,7 @@ pangene.")
            pybind11
            python
            sdsl-lite))
+    (properties '((tunable? . #t)))
     (home-page "https://github.com/vgteam/odgi")
     (synopsis "Optimized Dynamic Genome/Graph Implementation")
     (description "odgi provides an efficient and succinct dynamic DNA sequence
@@ -562,6 +571,7 @@ graph model, as well as algorithms for pangenome analysis.")
            zlib))
     (native-inputs
      (list perl))
+    (properties '((tunable? . #t)))
     (home-page "https://github.com/ekg/seqwish")
     (synopsis "Alignment to variation graph inducer")
     (description "Seqwish implements a lossless conversion from pairwise