From add8bb0bdf3797704a30095ef21058b11778bc27 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Wed, 22 Mar 2023 14:22:33 +0200
Subject: bh20-seq-resource: Patch reference to minimap2.

* gn/packages/bioinformatics.scm (bh20-seq-resource)[arguments]: Add
phase to hardcode path to minimap2.
[inputs]: Add minimap2.
---
 gn/packages/bioinformatics.scm | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 48f1c40..b94f537 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1812,7 +1812,16 @@ suitable for long reads, but works also well with short reads.")
       (build-system python-build-system)
       (arguments
        (list
-         #:tests? #f))  ; Tests can't find pytest
+         #:tests? #f    ; Tests can't find pytest
+         #:phases
+         #~(modify-phases %standard-phases
+             (add-after 'unpack 'patch-program-calls
+               (lambda* (#:key inputs #:allow-other-keys)
+                 (substitute* "bh20sequploader/qc_fasta.py"
+                   (("\"minimap2\"")
+                    (string-append "\"" (search-input-file
+                                          inputs "/bin/minimap2")
+                                   "\""))))))))
       (propagated-inputs
        (list python-arvados-python-client
              python-schema-salad
@@ -1829,6 +1838,8 @@ suitable for long reads, but works also well with short reads.")
              ;; and for the service
              python
              gunicorn))
+      (inputs
+       (list minimap2))
       (native-inputs
        (list python-pytest-4                ; < 6
              python-pytest-runner-4))       ; < 5
-- 
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