Updated (gfautil) to latest rust packaging

1 files changed, 234 insertions, 247 deletions

diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm
index d63bcf2..41092bf 100644
--- a/gn/packages/pangenome-rust.scm
+++ b/gn/packages/pangenome-rust.scm
@@ -1230,7 +1230,7 @@
   ;; TODO: Define standalone package if this is a workspace.
   (origin
     (method git-fetch)
-    (uri (git-reference (url "https://github.com/chfi/rs-handlegraph")
+    (uri (git-reference (url "https://github.com/pangenome/rs-handlegraph")
                         (commit "3ac575e4216ce16a16667503a8875e469a40a97a")))
     (file-name (git-file-name "rust-handlegraph" "0.7.0-alpha.9.3ac575e"))
     (sha256 (base32 "1x9lhc4hjyfixvhdxr6z0lanfcynnqsmx3dqaf6xw4dpx0i4mcgg"))))
@@ -1950,220 +1950,151 @@
 ;;; 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"))
+;;; New crate sources for gfautil 0.4.0-alpha.5
 
+(define rust-js-sys-0.3.94
+  (crate-source "js-sys" "0.3.94"
+                "1nb4fr7c78mrrdhmg04nbac1zvd5z3panvqka8sy30nfh3py411f"))
 (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-cc-1.2.58
+  (crate-source "cc" "1.2.58"
+                "1qb0zyqhn8pqzdp7d3scm19zmvgvbyh3iabmj1q7fc4ynva2isg1"))
 
-(define rust-handlegraph-0.3.0
-  (crate-source "handlegraph" "0.3.0"
-                "1sj100w4lpj7798pws85qrfrzsily5hhzh6j118rwf56sgic1yml"))
+(define rust-console-0.16.3
+  (crate-source "console" "0.16.3"
+                "11zwz1vnfr0nx6dyjx0gjymp8864y5hxwf01ynfd2s8kapsqlknn"))
 
-(define rust-heck-0.3.1
-  (crate-source "heck" "0.3.1"
-                "01a2v7yvkiqxakdqz4hw3w3g4sm52ivz9cs3qcsv2arxsmw4wmi0"))
+(define rust-env-logger-0.7.1
+  (crate-source "env_logger" "0.7.1"
+                "0djx8h8xfib43g5w94r1m1mkky5spcw4wblzgnhiyg5vnfxknls4"))
 
-(define rust-hermit-abi-0.1.14
-  (crate-source "hermit-abi" "0.1.14"
-                "02brqrk80xjk343i9a88m5m1c4czzj9dvd63id4kqsyfsknnwn5r"))
+(define rust-fixedbitset-0.2.0
+  (crate-source "fixedbitset" "0.2.0"
+                "0kg03p777wc0dajd9pvlcnsyrwa8dhqwf0sd9r4dw0p82rs39arp"))
 
-(define rust-lazy-static-1.4.0
-  (crate-source "lazy_static" "1.4.0"
-                "0in6ikhw8mgl33wjv6q6xfrb5b9jr16q8ygjy803fay4zcisvaz2"))
+(define rust-fxhash-0.2.1
+  (crate-source "fxhash" "0.2.1"
+                "037mb9ichariqi45xm6mz0b11pa92gj38ba0409z3iz239sns6y3"))
 
-(define rust-lexical-core-0.7.4
-  (crate-source "lexical-core" "0.7.4"
-                "05i6b69ay8xbxw88vx89vglb7xm5n8ky82hax7d5a7z60bdccrfv"))
+(define rust-handlegraph-0.7.0-alpha.9
+  (crate-source "handlegraph" "0.7.0-alpha.9"
+                "1frlcdwhycjvizb0gfb0v36vxjdi0jxagl2l2v6dzdjxpaawv9rs"))
 
-(define rust-libc-0.2.71
-  (crate-source "libc" "0.2.71"
-                "0jbgi25rhglhvpxv62alyzyral6601kldmlhbxim4w6j15jv0mwl"))
+(define rust-humantime-1.3.0
+  (crate-source "humantime" "1.3.0"
+                "0krwgbf35pd46xvkqg14j070vircsndabahahlv3rwhflpy4q06z"))
 
-(define rust-maybe-uninit-2.0.0
-  (crate-source "maybe-uninit" "2.0.0"
-                "004y0nzmpfdrhz251278341z6ql34iv1k6dp1h6af7d6nd6jwc30"))
+(define rust-indexmap-1.9.3
+  (crate-source "indexmap" "1.9.3"
+                "16dxmy7yvk51wvnih3a3im6fp5lmx0wx76i03n06wyak6cwhw1xx"))
 
-(define rust-memchr-2.3.3
-  (crate-source "memchr" "2.3.3"
-                "0074pvsfl938ndl5js14ibc7i9q0k3zp390z843w8nlyv4bxha1p"))
+(define rust-indicatif-0.15.0
+  (crate-source "indicatif" "0.15.0"
+                "1r4n50mclyi4c7b9c9mlma1rhchjamw71r3z8vgqcmp24mhvbakv"))
 
-(define rust-memoffset-0.5.5
-  (crate-source "memoffset" "0.5.5"
-                "0pz55g763c113fffqbhdbdzjd8n4kq7wdillgs9qmw5vw4kb1661"))
+(define rust-itoa-1.0.18
+  (crate-source "itoa" "1.0.18"
+                "10jnd1vpfkb8kj38rlkn2a6k02afvj3qmw054dfpzagrpl6achlg"))
 
-(define rust-nom-5.1.2
-  (crate-source "nom" "5.1.2"
-                "1br74rwdp3c2ddga03bphnf355spn4mzwf1slg0a30zd4qnjdd7z"))
+(define rust-number-prefix-0.3.0
+  (crate-source "number_prefix" "0.3.0"
+                "0slm4mqmpgs6hvz22ycny9lvyvl9ivs80a1lncslp7lszz02zc0p"))
 
-(define rust-num-cpus-1.13.0
-  (crate-source "num_cpus" "1.13.0"
-                "1cv6yxhz2zbnwn8pn1yn8grg7zsnd523947fby41a737aqvryj85"))
+(define rust-once-cell-1.21.4
+  (crate-source "once_cell" "1.21.4"
+                "0l1v676wf71kjg2khch4dphwh1jp3291ffiymr2mvy1kxd5kwz4z"))
 
-(define rust-proc-macro-error-1.0.3
-  (crate-source "proc-macro-error" "1.0.3"
-                "103qvh4qzlhxgpghl75yr82p9672ngwfi1454hknc4f3fybmw5zw"))
+(define rust-petgraph-0.5.1
+  (crate-source "petgraph" "0.5.1"
+                "1dzxda6z17sfxly11m8ja3iargh73pw0s1sdgjyp0qp5dm51cza6"))
 
-(define rust-proc-macro-error-attr-1.0.3
-  (crate-source "proc-macro-error-attr" "1.0.3"
-                "0l2w8caxbx5n30qx3pgj6hzmlcy2gzd3cjf4bql83dbyl5f7kj9w"))
+(define rust-pretty-env-logger-0.4.0
+  (crate-source "pretty_env_logger" "0.4.0"
+                "17gva1rlf9fhgr0jr19kv39f8bir3f4pa4jz02qbhl9qanwkcvcj"))
 
-(define rust-proc-macro2-1.0.18
-  (crate-source "proc-macro2" "1.0.18"
-                "1yn8szcbnm9j2sw427vpf603xjg6v27hfny40ifzdc8nm0qn7bmy"))
+(define rust-saboten-0.1.2-alpha.3
+  (crate-source "saboten" "0.1.2-alpha.3"
+                "17l2njxzjb4d9gp536qp0ciqdy0ljg6wi80c7r3xk8lnsz9lwa66"))
 
-(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-strsim-0.8.0
+  (crate-source "strsim" "0.8.0"
+                "0sjsm7hrvjdifz661pjxq5w4hf190hx53fra8dfvamacvff139cf"))
 
-(define rust-regex-automata-0.1.9
-  (crate-source "regex-automata" "0.1.9"
-                "1r3aqa9c0s9sfrmd2w0mli16ldjzbar0rzb1x7srfjkasrqys7df"))
+(define rust-textwrap-0.11.0
+  (crate-source "textwrap" "0.11.0"
+                "0q5hky03ik3y50s9sz25r438bc4nwhqc6dqwynv4wylc807n29nk"))
 
-(define rust-regex-syntax-0.6.18
-  (crate-source "regex-syntax" "0.6.18"
-                "1s648w7rwpxnq9iqwbyy43ar4al07906jpz0jxlql23bgjwjwh96"))
+(define rust-three-edge-connected-0.2.2
+  (crate-source "three-edge-connected" "0.2.2"
+                "0z9mqq013dqfgdj740sgkahrm6navrbd948w8rwax6sp0059bkqg"))
 
-(define rust-ryu-1.0.5
-  (crate-source "ryu" "1.0.5"
-                "0vpqv1dj7fksa6hm3zpk5rbsjs0ifbfy7xwzsyyil0rx37a03lvi"))
+(define rust-vec-map-0.8.2
+  (crate-source "vec_map" "0.8.2"
+                "1481w9g1dw9rxp3l6snkdqihzyrd2f8vispzqmwjwsdyhw8xzggi"))
 
-(define rust-scopeguard-1.1.0
-  (crate-source "scopeguard" "1.1.0"
-                "1kbqm85v43rq92vx7hfiay6pmcga03vrjbbfwqpyj3pwsg3b16nj"))
+(define rust-wasm-bindgen-0.2.117
+  (crate-source "wasm-bindgen" "0.2.117"
+                "1c6hi55mq70546hrvrx7wa27sn3yvf04gg6hf8riwn8mnhdzql85"))
 
-(define rust-serde-1.0.114
-  (crate-source "serde" "1.0.114"
-                "1lwcxlh8c09cs6qmwr6w68hl989mczwmwrzgc3p7hl0aixcgf5sk"))
+(define rust-wasm-bindgen-macro-0.2.117
+  (crate-source "wasm-bindgen-macro" "0.2.117"
+                "1gl6gqy60khhyqv354m0kmgk541sass8kzymxim7hi6zbaizkgbz"))
 
-(define rust-serde-derive-1.0.114
-  (crate-source "serde_derive" "1.0.114"
-                "13lgjxsc617yhblm779jwg43gxab2dfgrpyd6znvl3v90i5yj2ra"))
+(define rust-wasm-bindgen-macro-support-0.2.117
+  (crate-source "wasm-bindgen-macro-support" "0.2.117"
+                "1wlza8xdr18cac2wm3ahxdwx1nnqa01m0d3jf3kd9dmsy8z6kafw"))
 
-(define rust-strsim-0.8.0
-  (crate-source "strsim" "0.8.0"
-                "0sjsm7hrvjdifz661pjxq5w4hf190hx53fra8dfvamacvff139cf"))
+(define rust-wasm-bindgen-shared-0.2.117
+  (crate-source "wasm-bindgen-shared" "0.2.117"
+                "0frxrdi1w0cswv8v7n1972hd23nbwm8hr7a2dhdq8bbd59l9l4ir"))
 
-(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-ansi-term-0.12.1
+  (crate-source "ansi_term" "0.12.1"
+                "1ljmkbilxgmhavxvxqa7qvm6f3fjggi7q2l3a72q9x0cxjvrnanm"))
 
-(define rust-syn-1.0.33
-  (crate-source "syn" "1.0.33"
-                "1kdj0piws00cc0rgn2315625dfxfpxrzf6gib5lms05viipdkmg8"))
+(define rust-clap-2.34.0
+  (crate-source "clap" "2.34.0"
+                "071q5d8jfwbazi6zhik9xwpacx5i6kb2vkzy060vhf0c3120aqd0"))
 
-(define rust-syn-mid-0.5.0
-  (crate-source "syn-mid" "0.5.0"
-                "12ikg5jfklixq0wsgfl7sdzjqlxgq50ygklxy4f972hjdjgm7qvv"))
+(define rust-heck-0.3.3
+  (crate-source "heck" "0.3.3"
+                "0b0kkr790p66lvzn9nsmfjvydrbmh9z5gb664jchwgw64vxiwqkd"))
 
-(define rust-textwrap-0.11.0
-  (crate-source "textwrap" "0.11.0"
-                "0q5hky03ik3y50s9sz25r438bc4nwhqc6dqwynv4wylc807n29nk"))
+(define rust-hermit-abi-0.1.19
+  (crate-source "hermit-abi" "0.1.19"
+                "0cxcm8093nf5fyn114w8vxbrbcyvv91d4015rdnlgfll7cs6gd32"))
 
-(define rust-thread-local-1.0.1
-  (crate-source "thread_local" "1.0.1"
-                "054vlrr1vsdy1h4b7n99mr24pnj8928ig9qwzg36wnkld4dns36l"))
+(define rust-libc-0.2.184
+  (crate-source "libc" "0.2.184"
+                "1bz4525m7lwzr63iidh7lp9ppz2c9va1pn6fyjh5wsp1ajjd5xa8"))
 
-(define rust-unicode-segmentation-1.6.0
-  (crate-source "unicode-segmentation" "1.6.0"
-                "1h7d48mzpi8hwf5cvnq07warkv86pvapzzzf32hvbjsk20yiagp8"))
+(define rust-proc-macro-error-1.0.4
+  (crate-source "proc-macro-error" "1.0.4"
+                "1373bhxaf0pagd8zkyd03kkx6bchzf6g0dkwrwzsnal9z47lj9fs"))
 
-(define rust-unicode-width-0.1.8
-  (crate-source "unicode-width" "0.1.8"
-                "1qxizyi6xbcqyi4z79p523ywvmgsfcgfqb3zv3c8i6x1jcc5jdwk"))
+(define rust-proc-macro-error-attr-1.0.4
+  (crate-source "proc-macro-error-attr" "1.0.4"
+                "0sgq6m5jfmasmwwy8x4mjygx5l7kp8s4j60bv25ckv2j1qc41gm1"))
 
-(define rust-unicode-xid-0.2.1
-  (crate-source "unicode-xid" "0.2.1"
-                "0r6mknipyy9vpz8mwmxvkx65ff2ha1n2pxqjj6f46lcn8yrhpzpp"))
+(define rust-structopt-0.3.26
+  (crate-source "structopt" "0.3.26"
+                "043sg3qxllann6q9i71d05qp3q13scmcvhxhd950ka2v8ij5qsqc"))
 
-(define rust-vec-map-0.8.2
-  (crate-source "vec_map" "0.8.2"
-                "1481w9g1dw9rxp3l6snkdqihzyrd2f8vispzqmwjwsdyhw8xzggi"))
+(define rust-structopt-derive-0.4.18
+  (crate-source "structopt-derive" "0.4.18"
+                "1q5gcigmvw0cinjxzpyrkflliq5r1ivljmrvfrl3phcwgwraxdfw"))
 
-(define rust-version-check-0.9.2
-  (crate-source "version_check" "0.9.2"
-                "1vbaqdf802qinsq8q20w8w0qn2pv0rkq5p73ijcblrwxcvjp5adm"))
+(define rust-unicode-segmentation-1.13.2
+  (crate-source "unicode-segmentation" "1.13.2"
+                "135a26m4a0wj319gcw28j6a5aqvz00jmgwgmcs6szgxjf942facn"))
 
+(define rust-unicode-width-0.1.14
+  (crate-source "unicode-width" "0.1.14"
+                "1bzn2zv0gp8xxbxbhifw778a7fc93pa6a1kj24jgg9msj07f7mkx"))
 
 (define-cargo-inputs lookup-cargo-inputs
   (gfainject =>
@@ -2838,63 +2769,115 @@
           rust-wit-component-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
+    (list rust-aho-corasick-1.1.4
+          rust-android-system-properties-0.1.5
+          rust-ansi-term-0.12.1
+          rust-anyhow-1.0.102
+          rust-arrayvec-0.5.2
           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-autocfg-1.5.0
+          rust-bitflags-1.3.2
+          rust-boomphf-0.5.9
+          rust-bstr-0.2.17
+          rust-bumpalo-3.20.2
+          rust-bytemuck-1.25.0
+          rust-bytemuck-derive-1.10.2
+          rust-byteorder-1.5.0
+          rust-cc-1.2.58
+          rust-cfg-if-1.0.4
+          rust-chrono-0.4.44
+          rust-clap-2.34.0
+          rust-console-0.16.3
+          rust-core-foundation-sys-0.8.7
+          rust-crossbeam-channel-0.5.15
+          rust-crossbeam-deque-0.8.6
+          rust-crossbeam-epoch-0.9.18
+          rust-crossbeam-utils-0.8.21
+          rust-either-1.15.0
+          rust-encode-unicode-1.0.0
+          rust-env-logger-0.7.1
+          rust-find-msvc-tools-0.1.9
+          rust-fixedbitset-0.2.0
+          rust-fnv-1.0.7
+          rust-fxhash-0.2.1
+          rust-gfa-0.10.1
+          rust-handlegraph-0.7.0-alpha.9
+          rust-hashbrown-0.12.3
+          rust-heck-0.3.3
+          rust-hermit-abi-0.1.19
+          rust-humantime-1.3.0
+          rust-iana-time-zone-0.1.65
+          rust-iana-time-zone-haiku-0.1.2
+          rust-indexmap-1.9.3
+          rust-indicatif-0.15.0
+          rust-itoa-1.0.18
+          rust-js-sys-0.3.94
+          rust-lazy-static-1.5.0
+          rust-lexical-core-0.7.6
+          rust-libc-0.2.184
+          rust-log-0.4.29
+          rust-memchr-2.8.0
+          rust-memmap-0.7.0
+          rust-nom-5.1.3
+          rust-num-traits-0.2.19
+          rust-number-prefix-0.3.0
+          rust-once-cell-1.21.4
+          rust-petgraph-0.5.1
+          rust-pretty-env-logger-0.4.0
+          rust-proc-macro-error-1.0.4
+          rust-proc-macro-error-attr-1.0.4
+          rust-proc-macro2-1.0.106
+          rust-quick-error-1.2.3
+          rust-quote-1.0.45
+          rust-rand-core-0.6.4
+          rust-rayon-1.11.0
+          rust-rayon-core-1.13.0
+          rust-regex-1.12.3
+          rust-regex-automata-0.1.10
+          rust-regex-automata-0.4.14
+          rust-regex-syntax-0.8.10
+          rust-rustc-hash-1.1.0
+          rust-rustversion-1.0.22
+          rust-ryu-1.0.23
+          rust-saboten-0.1.2-alpha.3
+          rust-serde-1.0.228
+          rust-serde-core-1.0.228
+          rust-serde-derive-1.0.228
+          rust-serde-json-1.0.149
+          rust-shlex-1.3.0
           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-structopt-0.3.26
+          rust-structopt-derive-0.4.18
+          rust-succinct-0.5.2
+          rust-syn-1.0.109
+          rust-syn-2.0.117
+          rust-termcolor-1.4.1
           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-three-edge-connected-0.2.2
+          rust-unicode-ident-1.0.24
+          rust-unicode-segmentation-1.13.2
+          rust-unicode-width-0.1.14
+          rust-unicode-width-0.2.2
           rust-vec-map-0.8.2
-          rust-version-check-0.9.2
+          rust-version-check-0.9.5
+          rust-wasm-bindgen-0.2.117
+          rust-wasm-bindgen-macro-0.2.117
+          rust-wasm-bindgen-macro-support-0.2.117
+          rust-wasm-bindgen-shared-0.2.117
           rust-winapi-0.3.9
           rust-winapi-i686-pc-windows-gnu-0.4.0
-          rust-winapi-x86-64-pc-windows-gnu-0.4.0)))
+          rust-winapi-util-0.1.11
+          rust-winapi-x86-64-pc-windows-gnu-0.4.0
+          rust-windows-core-0.62.2
+          rust-windows-implement-0.60.2
+          rust-windows-interface-0.59.3
+          rust-windows-link-0.2.1
+          rust-windows-result-0.4.1
+          rust-windows-strings-0.5.1
+          rust-windows-sys-0.61.2
+          rust-wyhash-0.5.0
+          rust-zmij-1.0.21)))
 
 ;;;
 ;;; Main package.
@@ -2909,7 +2892,7 @@
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
-                      (url "https://github.com/chfi/gfainject")
+                      (url "https://github.com/pangenome/gfainject")
                       (commit commit)))
                 (file-name (git-file-name name version))
                 (sha256
@@ -2919,7 +2902,7 @@
       (arguments (list #:install-source? #f))
       ;; No upstream test data; tests require GFA/BAM input files.
       (inputs (cargo-inputs 'gfainject #:module '(gn packages pangenome-rust)))
-      (home-page "https://github.com/chfi/gfainject")
+      (home-page "https://github.com/pangenome/gfainject")
       (synopsis "Map BAM alignments to GFA graph paths as GAF records")
       (description
        "Gfainject maps read alignments from a BAM file to reference paths in a
@@ -3242,7 +3225,7 @@ sequences to accelerate the alignment process.")
                   (("git = \"https://github.com/AndreaGuarracino/tracepoints\", rev = \"b73773433561fb36f21136776a7297c5877ab593\"")
                    "path = \"guix-vendor/rust-tracepoints-0.1.0.b737734-checkout\", version = \"0.1.0\"")
                   ;; handlegraph
-                  (("git = \"https://github.com/chfi/rs-handlegraph\", rev = \"3ac575e4216ce16a16667503a8875e469a40a97a\"")
+                  (("git = \"https://github.com/pangenome/rs-handlegraph\", rev = \"3ac575e4216ce16a16667503a8875e469a40a97a\"")
                    "path = \"guix-vendor/rust-handlegraph-0.7.0-alpha.9.3ac575e-checkout\", version = \"0.7.0-alpha.9\"")
                   ;; sweepga
                   (("git = \"https://github.com/pangenome/sweepga\", rev = \"f5918434c1abadfad594b40392ad7c43e0da4af8\", default-features = false")
@@ -3367,22 +3350,26 @@ 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,
+  (let ((commit "5f7aea585126d07506031af8dedf12c60c7bb6a0")
+        (revision "0"))
+    (package
+      (name "gfautil")
+      (version (git-version "0.4.0-alpha.5" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/pangenome/rs-gfa-utils.git")
+                       (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0r51kz2vwmj8kkxr1az45g68m0acn652mcddsscc78m78yxh85v1"))))
+      (build-system cargo-build-system)
+      (arguments (list #:install-source? #f))
+      (inputs (cargo-inputs 'gfautil #:module '(gn packages pangenome-rust)))
+      (home-page "https://github.com/pangenome/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)))
+      (license license:expat))))