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authorEfraim Flashner2023-09-26 16:18:12 +0300
committerEfraim Flashner2023-09-26 16:18:12 +0300
commit0d8ed9f6c2ca7804a73028c947db0a2a6a61e7cb (patch)
tree23c803ed8c0654d95f6b3b274a993cfdb1433b20 /gn/packages
parenta848475c6bf6321dde971528f7c8d0c4d6e9e0d5 (diff)
downloadguix-bioinformatics-0d8ed9f6c2ca7804a73028c947db0a2a6a61e7cb.tar.gz
pggb: wrap with more packages
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/bioinformatics.scm13
1 files changed, 11 insertions, 2 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 95dda00..535018b 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -2692,7 +2692,11 @@ multiple sequence alignment.")
("scripts" "bin/scripts"))
#:phases
#~(modify-phases %standard-phases
- (add-before 'install 'patch-binary-path
+ (add-after 'unpack 'force-python3
+ (lambda _
+ (substitute* (find-files "scripts" "\\.py$")
+ (("/usr/bin/python") "/usr/bin/python3"))))
+ (add-before 'install 'patch-and-wrap-scripts
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "scripts/vcf_preprocess.sh"
(("bcftools ")
@@ -2706,6 +2710,8 @@ multiple sequence alignment.")
(for-each
(lambda (file)
(wrap-script file
+ `("R_LIBS_SITE" ":" prefix
+ (,(getenv "R_LIBS_SITE")))
`("PATH" ":" prefix
,(map (lambda (input) (string-append input "/bin"))
'#$(map (lambda (label)
@@ -2722,7 +2728,9 @@ multiple sequence alignment.")
"pafplot"
"parallel"
"pigz"
+ "python"
"r-data-table"
+ "r-minimal"
"rtg-tools"
"samtools"
"seqwish"
@@ -2756,9 +2764,10 @@ multiple sequence alignment.")
pafplot
parallel
pigz
+ python
python-igraph
- python-wrapper
r-data-table
+ r-minimal
rtg-tools
samtools
seqwish