diff options
| -rw-r--r-- | README.org | 60 | ||||
| -rw-r--r-- | gn/packages/gemma.scm | 60 |
2 files changed, 108 insertions, 12 deletions
@@ -58,31 +58,69 @@ Install slurm with ClusterName=(null) NodeName=selinunte CPUs=4 Boards=1 SocketsPerBoard=1 CoresPerSocket=2 ThreadsPerCore=2 RealMemory=7890 TmpDisk=29909 #+END_SRC -* Module system -Install the module environment with +* Common Workflow Language (CWL) + +Install the common workflow language tool cwltool from this repo with #+BEGIN_SRC bash + guix pull - guix package -i environment-modules + export PATH=$HOME/.config/guix/current/bin/guix:$PATH + ~/guix-bioinformatics$ env GUIX_PACKAGE_PATH=.:../guix-past/modules/ ~/.config/guix/current/bin/guix package -i cwl-runner -p ~/opt/CWL - modulecmd --version - VERSION=3.2.10 - DATE=2012-12-21 +The following package will be installed: + cwl-runner 1.0 + +The following derivations will be built: + /gnu/store/ld59374zr45rbqanh7ccfi2wa4d5x4yl-cwl-runner-1.0.drv + /gnu/store/86j15mxj5zp3k3sjimhqhb6zsj19azsf-python-schema-salad-7.0.20200811075006.drv + /gnu/store/0q2ls0is3253r4gx6hs7kmvlcz412lh1-schema-salad-7.0.20200811075006.tar.gz.drv + /gnu/store/myj1365ph687ynahjhg6zqslrmd6zpjq-cwltool-3.0.20201117141248.drv + +source ~/opt/CWL/etc/profile +cwltool --version + /gnu/store/50mncjcgc8vmq5dfrh0pb82avbzy8c4r-cwltool-3.0.20201117141248/bin/.cwltool-real 3.0 #+END_SRC -* Common Workflow Language (CWL) +To run CWL definitions you can install tools in a Guix environment (avoiding +Docker). Say you need mafft in a workflow + +#+begin_src sh + ~/guix-bioinformatics$ env GUIX_PACKAGE_PATH=.:../guix-past/modules/ ~/.config/guix/current/bin/guix environment \ + guix --ad-hoc cwl-runner mafft +#+end_src -Install the common workflow language tool cwltool with +in the new shell you should be able to find both CWL and MAFFT: + +#+begin_src sh +ls $GUIX_ENVIRONMENT/bin/cwl* +/gnu/store/bhfc5rk29s38w9kgcl4zmcdlh369y9f9-profile/bin/cwl-runner +/gnu/store/bhfc5rk29s38w9kgcl4zmcdlh369y9f9-profile/bin/cwltool +ls $GUIX_ENVIRONMENT/bin/mafft +/gnu/store/bhfc5rk29s38w9kgcl4zmcdlh369y9f9-profile/bin/mafft +#+end_src + +The paths can be loaded into the shell with + +: source $GUIX_ENVIRONMENT/etc/profile + +* Module system + +For those who think they need modules: install the module environment +with #+BEGIN_SRC bash guix pull - guix package -i python2-cwltool + guix package -i environment-modules - cwtool --version - 1.0.20150916041152 + modulecmd --version + VERSION=3.2.10 + DATE=2012-12-21 #+END_SRC +Note that GNU Guix supercedes module functionality! + * Development tips ** Override individual packages diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm index 9bbb186..e6d49b4 100644 --- a/gn/packages/gemma.scm +++ b/gn/packages/gemma.scm @@ -100,7 +100,7 @@ (license license:bsd-3)))) -(define-public gemma-gn2 ; guix candidate - generic openblas version +(define-public gemma-gn2 ; Version used in GeneNetwork. Guix candidate - generic openblas version (let ((commit "97547ee82e0bd1cc2210612415b0ceb135dbba6d")) (package (name "gemma-gn2") @@ -176,6 +176,63 @@ genome-wide association studies (GWAS).") #:parallel-tests? #f)) )) +(define-public gemma-gn2-dev ; Dev version for GeneNetwork. Not a Guix candidate + (let ((commit "d53a04edc476d820de7a611cacc8b105115aa3cc")) + (package + (name "gemma-gn2-dev") + (version (string-append "0.98.2-" (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/genenetwork/GEMMA") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0xm4cjfzrcb1wc8lw9p1727spica8rlzwnvjkp7ackn1g7zmzhw0")))) + ; guix environment -C guix --ad-hoc gcc-toolchain gdb gsl openblas zlib bash ld-wrapper perl vim which + (inputs `( + ("gsl" ,gsl) + ("shunit2" ,shunit2) + ("openblas" ,openblas) + ("zlib" ,zlib) + )) + (native-inputs ; for running tests + `(("perl" ,perl) + ("which" ,which) + )) + + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'bin-mkdir + (lambda _ + (mkdir-p "bin") + )) + (replace 'build + (lambda* (#:key inputs #:allow-other-keys) + (invoke "make" "debug" "-j" (number->string (parallel-job-count))))) + (replace 'check + (lambda* (#:key inputs #:allow-other-keys) + (invoke "make" "fast-check" ))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file "bin/gemma" (string-append out "/bin")))))) + ; #:tests? #f + #:parallel-tests? #f)) + (home-page "http://www.xzlab.org/software.html") + (synopsis "Tool for genome-wide efficient mixed model association") + (description "Genome-wide Efficient Mixed Model Association (GEMMA) +provides a standard linear mixed model resolver with application in +genome-wide association studies (GWAS).") + + (license license:gpl3)))) + + + (define-public gemma-wrapper (package (name "gemma-wrapper") @@ -256,6 +313,7 @@ genome-wide association studies (GWAS).") (description "Gemma-development") (license license:gpl3)))) + (define-public faster-lmm-d-dev ; incomplete, just creates build environment (let ((commit "68e22043ce0ca348cbc4f3bdd015e036ba9ac5f2")) (package |