From 30e50263e965648d1236ad2b20a374ff89d5b151 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 7 Jun 2022 22:28:28 +0300
Subject: gn: hap.py: Add previously missing inputs.

---
 gn/packages/bioinformatics.scm | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 05ffb99..702f3e6 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -2425,7 +2425,7 @@ cases include:
               (for-each
                 (lambda (file)
                   (wrap-script file
-                    `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))
+                    `("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH")))
                     `("PATH" ":" prefix (,(string-append bcftools "/bin")
                                          ,(string-append samtools "/bin")))))
                 (find-files (string-append out "/bin") "\\.py$"))
@@ -2439,10 +2439,8 @@ cases include:
       ("python" ,python-2)
       ("python2-bx-python" ,python2-bx-python)
       ("python2-numpy" ,python2-numpy)
-
-      ;; TODO: re-package these!
-      ;("python2-pandas" ,python2-pandas)
-      ;("python2-pysam" ,python2-pysam)
+      ("python2-pandas" ,python2-pandas)
+      ("python2-pysam" ,(python2-package python-pysam))
       ("python2-scipy" ,python2-scipy)
       ("rtg-tools" ,rtg-tools)
       ("samtools" ,samtools)
-- 
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