diff options
| -rwxr-xr-x | .guix-shell | 2 | ||||
| -rw-r--r-- | gn/data/dataset.scm | 2 | ||||
| -rw-r--r-- | gn/data/genotype.scm | 2 | ||||
| -rw-r--r-- | guix.scm | 71 | ||||
| -rwxr-xr-x | scripts/precompute/precompute-hits.scm | 4 |
5 files changed, 78 insertions, 3 deletions
diff --git a/.guix-shell b/.guix-shell index f3c4ebc..0eb387b 100755 --- a/.guix-shell +++ b/.guix-shell @@ -2,6 +2,6 @@ # # . .guix-shell -- guile -L . --fresh-auto-compile --listen=1970 -echo "Create a shell to run tools. In the container" +echo "Create a shell to run tools." guix shell -C -D -F --network coreutils guile guile-dbi guile-dbd-mysql guile-fibers guile-json guile-gnutls guile-readline guile-redis openssl nss-certs gemma parallel $* diff --git a/gn/data/dataset.scm b/gn/data/dataset.scm index 5e81d1e..3d96663 100644 --- a/gn/data/dataset.scm +++ b/gn/data/dataset.scm @@ -1,5 +1,5 @@ (define-module (gn data dataset) - #:use-module (json) + ;; #:use-module (json) #:use-module (ice-9 match) #:use-module (ice-9 format) #:use-module (ice-9 iconv) diff --git a/gn/data/genotype.scm b/gn/data/genotype.scm index c7cb63c..a12deee 100644 --- a/gn/data/genotype.scm +++ b/gn/data/genotype.scm @@ -1,5 +1,5 @@ (define-module (gn data genotype) - #:use-module (json) + ;; #:use-module (json) #:use-module (ice-9 match) #:use-module (ice-9 format) #:use-module (ice-9 iconv) diff --git a/guix.scm b/guix.scm new file mode 100644 index 0000000..4417452 --- /dev/null +++ b/guix.scm @@ -0,0 +1,71 @@ +;; To use this file to build HEAD of gn-guile: +;; +;; guix build -f guix.scm +;; +;; To get a development container +;; +;; guix shell -C -D -f guix.scm +;; + +(use-modules + ((guix licenses) #:prefix license:) + (guix gexp) + (guix packages) + (guix git-download) + (guix build-system guile) + (gnu packages algebra) + (gnu packages base) + (gnu packages bash) + (gnu packages compression) + (gnu packages bioinformatics) + (gnu packages build-tools) + (gnu packages certs) + (gnu packages curl) + (gnu packages gcc) + (gnu packages guile) + (gnu packages guile-xyz) + (gnu packages llvm) + (gnu packages ninja) + (gnu packages parallel) + (gnu packages perl) + (gnu packages perl6) + (gnu packages pkg-config) + (gnu packages python) + (gnu packages tls) + (srfi srfi-1) + (ice-9 popen) + (ice-9 rdelim)) + +(define %source-dir (dirname (current-filename))) + +(define %git-commit + (read-string (open-pipe "git show HEAD | head -1 | cut -d ' ' -f 2" OPEN_READ))) + +(define-public gn-guile-git + (package + (name "gn-guile-git") + (version (git-version "4.0.0-" "HEAD" %git-commit)) + (source (local-file %source-dir #:recursive? #t)) + (build-system guile-build-system) + + (inputs + (list guile-3.0-latest bash-minimal perl + guile-dbi guile-dbd-mysql guile-fibers guile-gnutls guile-readline guile-redis openssl nss-certs gemma parallel)) + (propagated-inputs + (list guile-json-4)) + +#! + (arguments + `(#:compile-flags '("--r6rs" "-Wunbound-variable" "-Warity-mismatch") + #:modules ((guix build guile-build-system) + (guix build utils) + (srfi srfi-26) + (ice-9 ftw) + (json)))) +!# + (home-page "https://git.genenetwork.com/gn-guile") + (synopsis "Next generation GN code in guile") + (description "Use of guile.") + (license license:gpl3))) + +gn-guile-git diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm index 5f45967..8588061 100755 --- a/scripts/precompute/precompute-hits.scm +++ b/scripts/precompute/precompute-hits.scm @@ -6,6 +6,10 @@ and with some extra paths .guix-shell ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- guile -L . -s ./scripts/precompute/precompute-hits.scm +You may want to forward a mysql port if there is no DB locally + +ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org + !# (use-modules (dbi dbi) |