Working on cosigt and odgi (WIP)

1 files changed, 96 insertions, 28 deletions

diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
index 610d1aa..324019e 100644
--- a/gn/packages/pangenome.scm
+++ b/gn/packages/pangenome.scm
@@ -7,6 +7,7 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix gexp)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (gnu packages base)
@@ -18,7 +19,13 @@
   #:use-module (gnu packages image-processing)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages perl)
-  #:use-module (gnu packages pkg-config))
+  #:use-module (gnu packages cmake)
+  #:use-module (gnu packages datastructures)
+  #:use-module (gnu packages jemalloc)
+  #:use-module (gnu packages mpi)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-xyz))
 
 ;; gfautil has been moved to (gn packages pangenome-rust)
 
@@ -361,33 +368,41 @@ unmapped reads using unique k-mers from pangenome graph alleles.")
       (license license:expat))))
 
 (define-public cosigt
-  (package
-    (name "cosigt")
-    (version "0.1.7")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/davidebolo1993/cosigt")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "0hcmk520qs3iihdvzdyj46kf2gpqvqdr02klrlzzdjs7z5g1fmq4"))))
-    (build-system go-build-system)
-    (arguments
-     (list #:import-path "github.com/davidebolo1993/cosigt"
-           #:install-source? #f
-           #:phases
-           #~(modify-phases %standard-phases
-               (add-after 'install 'install-pipeline
-                 (lambda _
-                   (let ((share (string-append #$output "/share/cosigt")))
-                     (copy-recursively
-                      "src/github.com/davidebolo1993/cosigt/cosigt_smk"
-                      share)))))))
-    (inputs (list go-github-com-akamensky-argparse
-                  go-gonum-org-v1-gonum))
-    (home-page "https://github.com/davidebolo1993/cosigt")
+  (let ((commit "a8b8ec2f7b0ec01399a03afc032581bc3bcf4833")
+        (revision "1"))
+    (package
+      (name "cosigt")
+      (version (git-version "0.1.7" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/pjotrp/cosigt")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0rz2zvkfxi2b35bj019cmdm1vzbvfa1lyqsx7awwx3anr09dych1"))))
+      (build-system go-build-system)
+      (arguments
+       (list #:import-path "github.com/pjotrp/cosigt"
+             #:install-source? #f
+             #:phases
+             #~(modify-phases %standard-phases
+                 (add-after 'install 'install-pipeline
+                   (lambda _
+                     (let ((share (string-append #$output "/share/cosigt")))
+                       (copy-recursively
+                        "src/github.com/pjotrp/cosigt/cosigt_smk"
+                        share))))
+                 (add-after 'install 'install-tests
+                   (lambda _
+                     (let ((test (string-append #$output "/share/cosigt/test")))
+                       (copy-recursively
+                        "src/github.com/pjotrp/cosigt/test"
+                        test)))))))
+      (inputs (list go-github-com-akamensky-argparse
+                    go-gonum-org-v1-gonum))
+      (home-page "https://github.com/pjotrp/cosigt")
     (synopsis "Cosine similarity-based structural haplotype genotyper")
     (description
      "Cosigt (COsine SImilarity-based GenoTyper) assigns structural
@@ -396,4 +411,57 @@ Snakemake pipeline (@file{share/cosigt/}) and a genotyping binary.  Pipeline
 tools needed at runtime: snakemake, minimap2, samtools, bedtools, bwa-mem2,
 odgi, gafpack, gfainject, impg, pggb, meryl, kfilt, wally, miniprot, and
 pangene.")
+      (license license:expat))))
+
+(define-public odgi
+  (package
+    (name "odgi")
+    (version "0.9.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/pangenome/odgi/releases"
+                                  "/download/v" version
+                                  "/odgi-v" version ".tar.gz"))
+              (sha256
+               (base32 "0brg0sz45v1wv4ld3p4jwiab10nyp2f691zfwpiva6g6f71q3cbk"))
+              (snippet
+               #~(begin
+                   (use-modules (guix build utils))
+                   (substitute* "CMakeLists.txt"
+                     (("-march=native") "")
+                     (("-msse4\\.2") ""))))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+       #:tests? #f
+       #:parallel-build? #f ; OOM with parallel build
+       #:phases
+       #~(modify-phases %standard-phases
+           (add-after 'unpack 'use-gnuinstalldirs-macros
+             (lambda _
+               (substitute* "CMakeLists.txt"
+                 (("project\\(odgi\\)" all)
+                  (string-append all "\ninclude(GNUInstallDirs)"))
+                 (("LIBRARY DESTINATION lib")
+                  "LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}")
+                 (("ARCHIVE DESTINATION lib")
+                  "ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}"))))
+           (add-after 'unpack 'link-to-libodgi
+             (lambda _
+               (substitute* "CMakeLists.txt"
+                 (("^  \\$<TARGET_OBJECTS:odgi_objs>.*") "")
+                 (("target_link_libraries\\(odgi " all)
+                  (string-append all "libodgi_shared "))))))))
+    (native-inputs (list pkg-config))
+    (inputs
+     (list jemalloc
+           libdivsufsort
+           openmpi
+           pybind11
+           python
+           sdsl-lite))
+    (home-page "https://github.com/vgteam/odgi")
+    (synopsis "Optimized Dynamic Genome/Graph Implementation")
+    (description "odgi provides an efficient and succinct dynamic DNA sequence
+graph model, as well as algorithms for pangenome analysis.")
     (license license:expat)))