diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 13 |
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 |