Rename channels.scm to avoid guix pull compilation error [AI]

Rename manifest.scm to avoid guix pull compilation error [AI]

Replace local-file with git-fetch statements

5 files changed, 44 insertions, 19 deletions

diff --git a/README.org b/README.org
index 6e63108..5d7cc33 100644
--- a/README.org
+++ b/README.org
@@ -71,9 +71,9 @@ root with
 
 * Testing the build
 
-All important packages are listed in manifest.scm. Test with
+All important packages are listed in manifest.scm.example. Test with
 
-: guix build -L . -m manifest.scm
+: guix build -L . -m manifest.scm.example
 
 * An important note on AI
 
diff --git a/channels.scm b/channels.scm.example
index f7d1930..f7d1930 100644
--- a/channels.scm
+++ b/channels.scm.example
diff --git a/gn/packages/genenetwork-rust.scm b/gn/packages/genenetwork-rust.scm
index 54b8389..78e9130 100644
--- a/gn/packages/genenetwork-rust.scm
+++ b/gn/packages/genenetwork-rust.scm
@@ -555,13 +555,19 @@
 )
 
 (define-public rust-qtlreaper
+  (let ((commit "4dafa7289432d10685b6b235e3552ac3d681bb03")
+        (revision "0"))
   (package
     (name "rust-qtlreaper")
-    (version "0.1.4")
-    ;; Use local source with updated Cargo.lock for modern Rust.
-    ;; Push Cargo.lock upstream, then switch to git-fetch.
-    (source (local-file "/fast/pjotr/tmp/claude/factory/rust-qtlreaper"
-                        #:recursive? #t))
+    (version (git-version "0.1.4" revision commit))
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/genenetwork/rust-qtlreaper")
+                    (commit commit)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32 "1p7dmxh43ly0k7q6va0lzisqnk1i7af3dy5aw1sr4y5s7z0h6i0y"))))
     (build-system cargo-build-system)
     (arguments (list #:install-source? #f
                      #:tests? #f)) ; test results vary by machine
@@ -572,17 +578,22 @@
     (description
      "Rust-qtlreaper is a Rust implementation of QTL Reaper for mapping
 quantitative trait loci (QTL) in genetic datasets.")
-    (license license:agpl3+)))
+    (license license:agpl3+))))
 
 (define-public gn-rust-correlation
-  (let ((commit "48604d86471df965f189e46580578b24191add0e")
-        (revision "0"))
+  (let ((commit "473ad82b6f4477bbbeeef977e3e9f830f59a9b7f")
+        (revision "1"))
     (package
       (name "gn-rust-correlation")
       (version (git-version "0.1.4" revision commit))
-      ;; Use local source with updated Cargo.lock for modern Rust.
-      (source (local-file "/fast/pjotr/tmp/claude/factory/correlation_rust"
-                          #:recursive? #t))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/Alexanderlacuna/correlation_rust")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "1xlasa4ggyynmnm890i7zlsqds7jfclmh5s6p582xlfdf75k9h5z"))))
       (build-system cargo-build-system)
       (native-inputs (list gsl))
       (arguments (list #:install-source? #f))
diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm
index 913f7f3..7bd2d6b 100644
--- a/gn/packages/pangenome-rust.scm
+++ b/gn/packages/pangenome-rust.scm
@@ -3848,8 +3848,14 @@ collapses them into a non-redundant graph structure.")
     (package
       (name "gafpack")
       (version (git-version "0.0.0" revision commit))
-      (source (local-file "/fast/pjotr/tmp/claude/factory/gafpack"
-                          #:recursive? #t))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ekg/gafpack")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "0di2psh0ls7jlbnqs7k71p55f73pn23a09k1h3ril7gwjcrzr3rk"))))
       (build-system cargo-build-system)
       (arguments (list #:install-source? #f))
       (inputs (cargo-inputs 'gafpack #:module '(gn packages pangenome-rust)))
@@ -3861,11 +3867,19 @@ maps useful in haplotype-based genotyping.")
       (license license:expat))))
 
 (define-public vcfbub
+  (let ((commit "26a1f0cb216a423f8547c4ad0e0ce38cb9d324b9")
+        (revision "0"))
   (package
     (name "vcfbub")
-    (version "0.1.0")
-    (source (local-file "/fast/pjotr/tmp/claude/factory/vcfbub"
-                        #:recursive? #t))
+    (version (git-version "0.1.0" revision commit))
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pangenome/vcfbub")
+                    (commit commit)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32 "1j91b4mba0gpghix0sn6m6a81722vzhpf5a2b03ysrqsrvfykk5z"))))
     (build-system cargo-build-system)
     (arguments (list #:install-source? #f))
     (inputs (cargo-inputs 'vcfbub #:module '(gn packages pangenome-rust)))
@@ -3873,4 +3887,4 @@ maps useful in haplotype-based genotyping.")
     (synopsis "Popping bubbles in vg deconstruct VCFs")
     (description "vcfbub filters VCF records by snarl tree level and allele
 size, keeping nested bubbles when parent bubbles are popped.")
-    (license license:expat)))
+    (license license:expat))))
diff --git a/manifest.scm b/manifest.scm.example
index da257dc..da257dc 100644
--- a/manifest.scm
+++ b/manifest.scm.example