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authorEfraim Flashner2022-06-07 22:28:28 +0300
committerEfraim Flashner2022-06-07 22:28:28 +0300
commit30e50263e965648d1236ad2b20a374ff89d5b151 (patch)
tree613a644d8219d29c8426303ac87986971ac353ae /gn/packages/bioinformatics.scm
parent6642ad1162d80399649e7d2657f31e947bf7de84 (diff)
downloadguix-bioinformatics-30e50263e965648d1236ad2b20a374ff89d5b151.tar.gz
gn: hap.py: Add previously missing inputs.
Diffstat (limited to 'gn/packages/bioinformatics.scm')
-rw-r--r--gn/packages/bioinformatics.scm8
1 files changed, 3 insertions, 5 deletions
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)