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gnu: pigx-sars-cov-2: Update to 0.0.7. 

* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.7.
[inputs]: Remove bbmap and prinseq; add r-viridis.
[arguments]: Remove autoreconf phase.
Ricardo Wurmus 2022-05-06 14:11:18 +02:00
parent f550c0ccb0
commit 6f5cbac67d
No known key found for this signature in database
GPG Key ID: 197A5888235FACAC
1 changed files with 6 additions and 10 deletions
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@ -11310,23 +11310,20 @@ based methods.")
(define-public pigx-sars-cov-2 (define-public pigx-sars-cov-2
(package (package
(name "pigx-sars-cov-2") (name "pigx-sars-cov-2")
(version "0.0.5") (version "0.0.7")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_sarscov2_ww/" (uri (string-append "https://github.com/BIMSBbioinfo/pigx_sars-cov-2"
"releases/download/v" version "/releases/download/v" version
"/pigx_sars-cov2-ww-" version ".tar.gz")) "/pigx_sars-cov-2-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"1fkr9gp09zl5n7kdqmy9lrnq28k2z97wg74wgkyfssfyxvmq9cr2")))) "1bqm03ypf7l8lrkjkydxzn7vy0qlps3v9c5cpz2wb008zw44bi3k"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ;requires huge kraken database `(#:tests? #f ;requires huge kraken database
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(add-before 'bootstrap 'autoreconf
(lambda _
(invoke "autoreconf" "-vif")))
(add-before 'configure 'set-PYTHONPATH (add-before 'configure 'set-PYTHONPATH
(lambda _ (lambda _
(setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))))))
@ -11334,7 +11331,6 @@ based methods.")
(list automake autoconf)) (list automake autoconf))
(inputs (inputs
(list bash-minimal (list bash-minimal
bbmap
bedtools bedtools
bwa bwa
ensembl-vep ensembl-vep
@ -11345,7 +11341,6 @@ based methods.")
krona-tools krona-tools
lofreq lofreq
multiqc multiqc
prinseq
python-pyyaml python-pyyaml
python-wrapper python-wrapper
r-base64url r-base64url
@ -11361,6 +11356,7 @@ based methods.")
r-rmarkdown r-rmarkdown
r-stringr r-stringr
r-tidyr r-tidyr
r-viridis
samtools samtools
snakemake snakemake
wget)) wget))