Moved all pangenome Rust packages to pangenome-rust.scm

2 files changed, 297 insertions, 35 deletions

diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm
index 1d72cfa..d63bcf2 100644
--- a/gn/packages/pangenome-rust.scm
+++ b/gn/packages/pangenome-rust.scm
@@ -1950,6 +1950,221 @@
 ;;; Used by: (inputs (cargo-inputs 'impg #:module '(gn packages pangenome-rust)))
 ;;;
 
+;;; Crate sources for gfautil (generated by: guix import crate -f Cargo.lock gfautil).
+
+(define rust-aho-corasick-0.7.12
+  (crate-source "aho-corasick" "0.7.12"
+                "04fmv26hy41dr0ygpcm6z4vq64ly8q9zqwwvc0ysfsvhmi4afnf2"))
+
+(define rust-ansi-term-0.11.0
+  (crate-source "ansi_term" "0.11.0"
+                "16wpvrghvd0353584i1idnsgm0r3vchg8fyrm0x8ayv1rgvbljgf"))
+
+(define rust-arrayvec-0.5.1
+  (crate-source "arrayvec" "0.5.1"
+                "1f5mca8kiiwhvhxd1mbnq68j6v6rk139sch567zwwzl6hs37vxyg"))
+
+(define rust-atty-0.2.14
+  (crate-source "atty" "0.2.14"
+                "1s7yslcs6a28c5vz7jwj63lkfgyx8mx99fdirlhi9lbhhzhrpcyr"))
+
+(define rust-autocfg-1.0.0
+  (crate-source "autocfg" "1.0.0"
+                "17cv6pwb4q08s0ynpr4n8hv5299hcmhdgvdchzixfpw8y5qcgapq"))
+
+(define rust-bitflags-1.2.1
+  (crate-source "bitflags" "1.2.1"
+                "14qnd5nq8p2almk79m4m8ydqhd413yaxsyjp5xd19g3mikzf47fg"))
+
+(define rust-bstr-0.2.13
+  (crate-source "bstr" "0.2.13"
+                "0cd9gn35hb020r3zccmc2m710wavk2iyqn60j8aqgxqdnzywmb1i"))
+
+(define rust-bytemuck-1.3.1
+  (crate-source "bytemuck" "1.3.1"
+                "1scaac5xbfynzbpvz9yjbmg9ag2jalxfijapwlqh7xldf4li0ynv"))
+
+(define rust-byteorder-1.3.4
+  (crate-source "byteorder" "1.3.4"
+                "1pkjfhgjnq898g1d38ygcfi0msg3m6756cwv0sgysj1d26p8mi08"))
+
+(define rust-cfg-if-0.1.10
+  (crate-source "cfg-if" "0.1.10"
+                "08h80ihs74jcyp24cd75wwabygbbdgl05k6p5dmq8akbr78vv1a7"))
+
+(define rust-clap-2.33.1
+  (crate-source "clap" "2.33.1"
+                "0a91g4m6rcqpf6gzxh43cj6mnj9g8ahpr634baim6kcmgza81ymx"))
+
+(define rust-crossbeam-deque-0.7.3
+  (crate-source "crossbeam-deque" "0.7.3"
+                "11c2c0x5grdba3ah3g94yn6b8s47xi8qwm85h8hq5vmf9nbsy0lz"))
+
+(define rust-crossbeam-epoch-0.8.2
+  (crate-source "crossbeam-epoch" "0.8.2"
+                "1knsf0zz7rgzxn0nwz5gajjcrivxpw3zrdcp946gdhdgr9sd53h5"))
+
+(define rust-crossbeam-queue-0.2.3
+  (crate-source "crossbeam-queue" "0.2.3"
+                "0w15z68nz3ac4f2s4djhwha8vmlwsh9dlfrmsl4x84y2ah5acjvp"))
+
+(define rust-crossbeam-utils-0.7.2
+  (crate-source "crossbeam-utils" "0.7.2"
+                "1a31wbrda1320gj2a6az1lin2d34xfc3xf88da4c17qy5lxcgiy3"))
+
+(define rust-either-1.5.3
+  (crate-source "either" "1.5.3"
+                "1qyz1b1acad6w0k5928jw5zaq900zhsk7p8dlcp4hh61w4f6n7xv"))
+
+(define rust-gfa-0.6.2
+  (crate-source "gfa" "0.6.2"
+                "0ghmy4r0324s6vvmj9nmh326346nkwm7nybnpcpswnjvf02b85gw"))
+
+(define rust-handlegraph-0.3.0
+  (crate-source "handlegraph" "0.3.0"
+                "1sj100w4lpj7798pws85qrfrzsily5hhzh6j118rwf56sgic1yml"))
+
+(define rust-heck-0.3.1
+  (crate-source "heck" "0.3.1"
+                "01a2v7yvkiqxakdqz4hw3w3g4sm52ivz9cs3qcsv2arxsmw4wmi0"))
+
+(define rust-hermit-abi-0.1.14
+  (crate-source "hermit-abi" "0.1.14"
+                "02brqrk80xjk343i9a88m5m1c4czzj9dvd63id4kqsyfsknnwn5r"))
+
+(define rust-lazy-static-1.4.0
+  (crate-source "lazy_static" "1.4.0"
+                "0in6ikhw8mgl33wjv6q6xfrb5b9jr16q8ygjy803fay4zcisvaz2"))
+
+(define rust-lexical-core-0.7.4
+  (crate-source "lexical-core" "0.7.4"
+                "05i6b69ay8xbxw88vx89vglb7xm5n8ky82hax7d5a7z60bdccrfv"))
+
+(define rust-libc-0.2.71
+  (crate-source "libc" "0.2.71"
+                "0jbgi25rhglhvpxv62alyzyral6601kldmlhbxim4w6j15jv0mwl"))
+
+(define rust-maybe-uninit-2.0.0
+  (crate-source "maybe-uninit" "2.0.0"
+                "004y0nzmpfdrhz251278341z6ql34iv1k6dp1h6af7d6nd6jwc30"))
+
+(define rust-memchr-2.3.3
+  (crate-source "memchr" "2.3.3"
+                "0074pvsfl938ndl5js14ibc7i9q0k3zp390z843w8nlyv4bxha1p"))
+
+(define rust-memoffset-0.5.5
+  (crate-source "memoffset" "0.5.5"
+                "0pz55g763c113fffqbhdbdzjd8n4kq7wdillgs9qmw5vw4kb1661"))
+
+(define rust-nom-5.1.2
+  (crate-source "nom" "5.1.2"
+                "1br74rwdp3c2ddga03bphnf355spn4mzwf1slg0a30zd4qnjdd7z"))
+
+(define rust-num-cpus-1.13.0
+  (crate-source "num_cpus" "1.13.0"
+                "1cv6yxhz2zbnwn8pn1yn8grg7zsnd523947fby41a737aqvryj85"))
+
+(define rust-proc-macro-error-1.0.3
+  (crate-source "proc-macro-error" "1.0.3"
+                "103qvh4qzlhxgpghl75yr82p9672ngwfi1454hknc4f3fybmw5zw"))
+
+(define rust-proc-macro-error-attr-1.0.3
+  (crate-source "proc-macro-error-attr" "1.0.3"
+                "0l2w8caxbx5n30qx3pgj6hzmlcy2gzd3cjf4bql83dbyl5f7kj9w"))
+
+(define rust-proc-macro2-1.0.18
+  (crate-source "proc-macro2" "1.0.18"
+                "1yn8szcbnm9j2sw427vpf603xjg6v27hfny40ifzdc8nm0qn7bmy"))
+
+(define rust-quote-1.0.7
+  (crate-source "quote" "1.0.7"
+                "0drzd6pq7whq7qhdvvs8wn6pbb0hhc12pz8wv80fb05ixhbksmma"))
+
+(define rust-rayon-1.3.1
+  (crate-source "rayon" "1.3.1"
+                "104h6i5lcp9kx8g80jgqf6z7wcqa186q57wj4qzf011xfmb2iw32"))
+
+(define rust-rayon-core-1.7.1
+  (crate-source "rayon-core" "1.7.1"
+                "101jjwkcfw5jk31695gbdm163iicc2pz349q6l8lwj43j3c1abp9"))
+
+(define rust-regex-1.3.9
+  (crate-source "regex" "1.3.9"
+                "1rnqga94ypykl2apgj26l2j1s9bvr2ix4dlzs323n6abyky80dww"))
+
+(define rust-regex-automata-0.1.9
+  (crate-source "regex-automata" "0.1.9"
+                "1r3aqa9c0s9sfrmd2w0mli16ldjzbar0rzb1x7srfjkasrqys7df"))
+
+(define rust-regex-syntax-0.6.18
+  (crate-source "regex-syntax" "0.6.18"
+                "1s648w7rwpxnq9iqwbyy43ar4al07906jpz0jxlql23bgjwjwh96"))
+
+(define rust-ryu-1.0.5
+  (crate-source "ryu" "1.0.5"
+                "0vpqv1dj7fksa6hm3zpk5rbsjs0ifbfy7xwzsyyil0rx37a03lvi"))
+
+(define rust-scopeguard-1.1.0
+  (crate-source "scopeguard" "1.1.0"
+                "1kbqm85v43rq92vx7hfiay6pmcga03vrjbbfwqpyj3pwsg3b16nj"))
+
+(define rust-serde-1.0.114
+  (crate-source "serde" "1.0.114"
+                "1lwcxlh8c09cs6qmwr6w68hl989mczwmwrzgc3p7hl0aixcgf5sk"))
+
+(define rust-serde-derive-1.0.114
+  (crate-source "serde_derive" "1.0.114"
+                "13lgjxsc617yhblm779jwg43gxab2dfgrpyd6znvl3v90i5yj2ra"))
+
+(define rust-strsim-0.8.0
+  (crate-source "strsim" "0.8.0"
+                "0sjsm7hrvjdifz661pjxq5w4hf190hx53fra8dfvamacvff139cf"))
+
+(define rust-structopt-0.3.15
+  (crate-source "structopt" "0.3.15"
+                "0p06h59dpxb8y2rplb7h1pc0wpk2ikj77kmdcadhh1z8kqimwbyy"))
+
+(define rust-structopt-derive-0.4.8
+  (crate-source "structopt-derive" "0.4.8"
+                "0661n4qs9g0g51qwvmvj7dh2kiqmpw4jbdpazfj64rv1vvwi612i"))
+
+(define rust-syn-1.0.33
+  (crate-source "syn" "1.0.33"
+                "1kdj0piws00cc0rgn2315625dfxfpxrzf6gib5lms05viipdkmg8"))
+
+(define rust-syn-mid-0.5.0
+  (crate-source "syn-mid" "0.5.0"
+                "12ikg5jfklixq0wsgfl7sdzjqlxgq50ygklxy4f972hjdjgm7qvv"))
+
+(define rust-textwrap-0.11.0
+  (crate-source "textwrap" "0.11.0"
+                "0q5hky03ik3y50s9sz25r438bc4nwhqc6dqwynv4wylc807n29nk"))
+
+(define rust-thread-local-1.0.1
+  (crate-source "thread_local" "1.0.1"
+                "054vlrr1vsdy1h4b7n99mr24pnj8928ig9qwzg36wnkld4dns36l"))
+
+(define rust-unicode-segmentation-1.6.0
+  (crate-source "unicode-segmentation" "1.6.0"
+                "1h7d48mzpi8hwf5cvnq07warkv86pvapzzzf32hvbjsk20yiagp8"))
+
+(define rust-unicode-width-0.1.8
+  (crate-source "unicode-width" "0.1.8"
+                "1qxizyi6xbcqyi4z79p523ywvmgsfcgfqb3zv3c8i6x1jcc5jdwk"))
+
+(define rust-unicode-xid-0.2.1
+  (crate-source "unicode-xid" "0.2.1"
+                "0r6mknipyy9vpz8mwmxvkx65ff2ha1n2pxqjj6f46lcn8yrhpzpp"))
+
+(define rust-vec-map-0.8.2
+  (crate-source "vec_map" "0.8.2"
+                "1481w9g1dw9rxp3l6snkdqihzyrd2f8vispzqmwjwsdyhw8xzggi"))
+
+(define rust-version-check-0.9.2
+  (crate-source "version_check" "0.9.2"
+                "1vbaqdf802qinsq8q20w8w0qn2pv0rkq5p73ijcblrwxcvjp5adm"))
+
+
 (define-cargo-inputs lookup-cargo-inputs
   (gfainject =>
     (list rust-adler-1.0.2
@@ -2621,7 +2836,65 @@
           rust-wit-bindgen-rust-0.51.0
           rust-wit-bindgen-rust-macro-0.51.0
           rust-wit-component-0.244.0
-          rust-wit-parser-0.244.0)))
+          rust-wit-parser-0.244.0))
+  (gfautil =>
+    (list rust-aho-corasick-0.7.12
+          rust-ansi-term-0.11.0
+          rust-arrayvec-0.5.1
+          rust-atty-0.2.14
+          rust-autocfg-1.0.0
+          rust-bitflags-1.2.1
+          rust-bstr-0.2.13
+          rust-bytemuck-1.3.1
+          rust-byteorder-1.3.4
+          rust-cfg-if-0.1.10
+          rust-clap-2.33.1
+          rust-crossbeam-deque-0.7.3
+          rust-crossbeam-epoch-0.8.2
+          rust-crossbeam-queue-0.2.3
+          rust-crossbeam-utils-0.7.2
+          rust-either-1.5.3
+          rust-gfa-0.6.2
+          rust-handlegraph-0.3.0
+          rust-heck-0.3.1
+          rust-hermit-abi-0.1.14
+          rust-lazy-static-1.4.0
+          rust-lexical-core-0.7.4
+          rust-libc-0.2.71
+          rust-maybe-uninit-2.0.0
+          rust-memchr-2.3.3
+          rust-memoffset-0.5.5
+          rust-nom-5.1.2
+          rust-num-cpus-1.13.0
+          rust-proc-macro-error-1.0.3
+          rust-proc-macro-error-attr-1.0.3
+          rust-proc-macro2-1.0.18
+          rust-quote-1.0.7
+          rust-rayon-1.3.1
+          rust-rayon-core-1.7.1
+          rust-regex-1.3.9
+          rust-regex-automata-0.1.9
+          rust-regex-syntax-0.6.18
+          rust-ryu-1.0.5
+          rust-scopeguard-1.1.0
+          rust-serde-1.0.114
+          rust-serde-derive-1.0.114
+          rust-static-assertions-1.1.0
+          rust-strsim-0.8.0
+          rust-structopt-0.3.15
+          rust-structopt-derive-0.4.8
+          rust-syn-1.0.33
+          rust-syn-mid-0.5.0
+          rust-textwrap-0.11.0
+          rust-thread-local-1.0.1
+          rust-unicode-segmentation-1.6.0
+          rust-unicode-width-0.1.8
+          rust-unicode-xid-0.2.1
+          rust-vec-map-0.8.2
+          rust-version-check-0.9.2
+          rust-winapi-0.3.9
+          rust-winapi-i686-pc-windows-gnu-0.4.0
+          rust-winapi-x86-64-pc-windows-gnu-0.4.0)))
 
 ;;;
 ;;; Main package.
@@ -3092,3 +3365,24 @@ sequences to accelerate the alignment process.")
 sequences and their relative alignments and extracts sections of the sequences
 and alignments for analysis.  It can also compute graphs for the sequences.")
       (license license:expat))))
+
+(define-public gfautil
+  (package
+    (name "gfautil")
+    (version "0.1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (crate-uri "gfautil" version))
+        (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0cgiis9v1nd4m7zxvgsz8jf8ijv4d8fa5wb7cpnjshksb8z7xh69"))))
+    (build-system cargo-build-system)
+    (inputs (cargo-inputs 'gfautil #:module '(gn packages pangenome-rust)))
+    (home-page "https://github.com/chfi/rs-gfa-utils")
+    (synopsis "Command line tools for working with GFA files")
+    (description
+     "This package provides command line tools for working with @acronym{GFA,
+Graphical Fragment Assembly} files and related formats.")
+    (license license:expat)))
diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
index 93d66d0..610d1aa 100644
--- a/gn/packages/pangenome.scm
+++ b/gn/packages/pangenome.scm
@@ -7,10 +7,8 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix gexp)
-  #:use-module (guix build-system cargo)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
-  #:use-module (gnu packages)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages boost)
@@ -20,39 +18,9 @@
   #:use-module (gnu packages image-processing)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages perl)
-  #:use-module (gnu packages pkg-config)
-  #:use-module (past-crates packages crates-io)
-  #:use-module (gn packages crates-io))
+  #:use-module (gnu packages pkg-config))
 
-(define-public gfautil
-  (package
-    (name "gfautil")
-    (version "0.1.0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (crate-uri "gfautil" version))
-        (file-name
-         (string-append name "-" version ".tar.gz"))
-        (sha256
-         (base32
-          "0cgiis9v1nd4m7zxvgsz8jf8ijv4d8fa5wb7cpnjshksb8z7xh69"))))
-    (build-system cargo-build-system)
-    (arguments
-     `(#:cargo-inputs
-       (("rust-bstr" ,rust-bstr-0.2)
-        ("rust-clap" ,rust-clap-2)
-        ("rust-gfa" ,rust-gfa-0.6)
-        ("rust-handlegraph" ,rust-handlegraph-0.3)
-        ("rust-rayon" ,rust-rayon-1)
-        ("rust-serde" ,rust-serde-1)
-        ("rust-structopt" ,rust-structopt-0.3))))
-    (home-page "https://github.com/chfi/rs-gfa-utils")
-    (synopsis "Command line tools for working with GFA files")
-    (description
-     "This package provides command line tools for working with @acronym{GFA,
-Graphical Fragment Assembly} files and related formats.")
-    (license license:expat)))
+;; gfautil has been moved to (gn packages pangenome-rust)
 
 (define-public safestringlib
   (let ((commit "39219363f0497d04c710a1e11acdeb6d18d4b2f5")