Error: user-error ("Org export aborted. Unable to resolve link: \"introduction\"
See `org-export-with-broken-links'")
signal(user-error ("Org export aborted. Unable to resolve link: \"introduction\"\nSee `org-export-with-broken-links'"))
user-error("Org export aborted. Unable to resolve link: %S\nSee `org-export-with-broken-links'" "introduction")
org-export-data((link (:standard-properties [138 nil 155 167 169 0 nil nil nil nil nil nil nil nil # nil nil (paragraph (:standard-properties [138 138 138 170 170 0 nil nil nil nil nil nil nil nil # nil nil (item (:standard-properties [135 135 138 170 170 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) (plain-list (:standard-properties [135 135 135 309 310 1 nil planning nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) (section (:standard-properties [135 135 135 310 310 0 nil section nil nil nil 135 310 nil # nil nil (headline (:standard-properties [57 57 135 310 310 0 (:title) nil nil nil nil 137 308 1 # nil nil (org-data (:standard-properties [1 1 1 2040 2040 0 nil org-data nil nil nil 3 2040 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 57 57 0 nil first-section nil nil nil 1 57 nil # nil nil #30]) (keyword (:standard-properties [1 1 nil nil 57 1 nil top-comment nil nil nil nil nil nil # nil nil #33] :key "TITLE" :value "Installing GeneNetwork services with GNU Guix"))) #25 (headline (:standard-properties [310 310 326 557 557 0 (:title) nil nil nil nil 328 555 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [326 326 326 557 557 0 nil section nil nil nil 326 557 nil # nil nil #35]) (paragraph (:standard-properties [326 326 326 556 557 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Large system deployments tend to get very complex. In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #41)) (link (:standard-properties [479 nil 541 551 553 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #45))) #(").\n" 0 3 (:parent #41))))) (headline (:standard-properties [557 557 578 603 603 0 (:title) nil nil nil nil 580 601 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 19) t] :title (#("Binary deployment" 0 17 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [578 578 578 603 603 0 nil section nil nil nil 578 603 nil # nil nil #36]) (paragraph (:standard-properties [578 578 578 602 603 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("NYA (will go to README)\n" 0 24 (:parent #42))))) (headline (:standard-properties [603 603 629 1877 1877 0 (:title) nil nil nil nil 631 1875 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [629 629 629 1877 1877 0 nil section nil nil nil 629 1877 nil # nil nil #37]) (paragraph (:standard-properties [629 629 629 809 810 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("GNU Guix allows for " 0 20 (:parent #43)) (link (:standard-properties [649 nil 718 741 744 1 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #47))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #43))) (src-block (:standard-properties [810 810 nil nil 1016 1 nil nil nil nil nil nil nil nil # nil nil #40] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [1016 1016 1016 1191 1192 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #45)) (link (:standard-properties [1072 nil 1177 1187 1189 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #49))) #(".\n" 0 2 (:parent #45))) (paragraph (:standard-properties [1192 1192 1192 1255 1256 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #46))) (fixed-width (:standard-properties [1256 1256 nil nil 1312 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [1312 1312 1312 1315 1316 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("So\n" 0 3 (:parent #48))) (paragraph (:standard-properties [1316 1316 1316 1702 1703 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("#+begin" 0 7 (:parent #49)) (subscript (:standard-properties [1323 nil 1324 1327 1328 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("src" 0 3 (:parent #53))) #("sh :lang bash\n#+begin" 0 23 (:parent #49)) (subscript (:standard-properties [1351 nil 1352 1355 1356 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #49)) (subscript (:standard-properties [1396 nil 1397 1404 1404 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [1404 nil 1405 1409 1409 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #49)) (subscript (:standard-properties [1681 nil 1682 1685 1686 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("src" 0 3 (:parent #60))) #("sh :lang bash\n" 0 16 (:parent #49))) (paragraph (:standard-properties [1703 1703 1703 1716 1717 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Install with\n" 0 13 (:parent #50))) (paragraph (:standard-properties [1717 1717 1717 1876 1877 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("#+begin" 0 7 (:parent #51)) (subscript (:standard-properties [1724 nil 1725 1728 1729 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #51)) (subscript (:standard-properties [1769 nil 1770 1777 1777 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [1777 nil 1778 1782 1782 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2\n#+end" 0 73 (:parent #51)) (subscript (:standard-properties [1855 nil 1856 1859 1860 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("src" 0 3 (:parent #60))) #("sh :lang bash\n" 0 16 (:parent #51))))) (headline (:standard-properties [1877 1877 1895 2040 2040 0 (:title) nil nil nil nil 1897 2038 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 16) t] :title (#("Create archive" 0 14 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1895 1895 1895 2040 2040 0 nil section nil nil nil 1895 2040 nil # nil nil #38]) (fixed-width (:standard-properties [1895 1895 nil nil 2040 1 nil planning nil nil nil nil nil nil # nil nil #41] :value "env GUIX_PACKAGE_PATH=../../genenetwork/guix-bioinformatics/ ./pre-inst-env guix archive --export -r genenetwork2 > guix_gn2-2.0-9e9475053.nar")))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #25))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #20)]) #15)] :type unordered) #10 (item (:standard-properties [170 170 173 215 215 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #15] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [173 173 173 215 215 0 nil nil nil nil nil nil nil nil # nil nil #19]) (link (:standard-properties [173 nil 195 212 214 0 nil nil nil nil nil nil nil nil # nil nil #22] :type "custom-id" :type-explicit-p nil :path "binary-deployment" :format bracket :raw-link "#binary-deployment" :application nil :search-option nil) #("Binary deployment" 0 17 (:parent #25))) #("\n" 0 1 (:parent #22)))) (item (:standard-properties [215 215 218 270 270 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #15] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [218 218 218 270 270 0 nil nil nil nil nil nil nil nil # nil nil #20]) (link (:standard-properties [218 nil 245 267 269 0 nil nil nil nil nil nil nil nil # nil nil #23] :type "custom-id" :type-explicit-p nil :path "from-source-deployment" :format bracket :raw-link "#from-source-deployment" :application nil :search-option nil) #("From source deployment" 0 22 (:parent #26))) #("\n" 0 1 (:parent #23)))) (item (:standard-properties [270 270 273 309 309 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #15] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [273 273 273 309 309 0 nil nil nil nil nil nil nil nil # nil nil #21]) (link (:standard-properties [273 nil 292 306 308 0 nil nil nil nil nil nil nil nil # nil nil #24] :type "custom-id" :type-explicit-p nil :path "create-archive" :format bracket :raw-link "#create-archive" :application nil :search-option nil) #("Create archive" 0 14 (:parent #27))) #("\n" 0 1 (:parent #24)))))] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) #5)]) #0 #("\n" 0 1 (:parent #5)))] :type "custom-id" :type-explicit-p nil :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil) #("Introduction" 0 12 (:parent #0))) (:export-options (body-only) :back-end #s(org-export-backend :name html :parent nil :transcoders ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :options ((:html-doctype "HTML_DOCTYPE" nil org-html-doctype) (:html-container "HTML_CONTAINER" nil org-html-container-element) (:html-content-class "HTML_CONTENT_CLASS" nil org-html-content-class) (:description "DESCRIPTION" nil nil newline) (:keywords "KEYWORDS" nil nil space) (:html-html5-fancy nil "html5-fancy" org-html-html5-fancy) (:html-link-use-abs-url nil "html-link-use-abs-url" org-html-link-use-abs-url) (:html-link-home "HTML_LINK_HOME" nil org-html-link-home) (:html-link-up "HTML_LINK_UP" nil org-html-link-up) (:html-mathjax "HTML_MATHJAX" nil "" space) (:html-equation-reference-format "HTML_EQUATION_REFERENCE_FORMAT" nil org-html-equation-reference-format t) (:html-postamble nil "html-postamble" org-html-postamble) (:html-preamble nil "html-preamble" org-html-preamble) (:html-head "HTML_HEAD" nil org-html-head newline) (:html-head-extra "HTML_HEAD_EXTRA" nil org-html-head-extra newline) (:subtitle "SUBTITLE" nil nil parse) (:html-head-include-default-style nil "html-style" org-html-head-include-default-style) (:html-head-include-scripts nil "html-scripts" org-html-head-include-scripts) (:html-allow-name-attribute-in-anchors nil nil org-html-allow-name-attribute-in-anchors) (:html-divs nil nil org-html-divs) (:html-checkbox-type nil nil org-html-checkbox-type) (:html-extension nil nil org-html-extension) (:html-footnote-format nil nil org-html-footnote-format) (:html-footnote-separator nil nil org-html-footnote-separator) (:html-footnotes-section nil nil org-html-footnotes-section) (:html-format-drawer-function nil nil org-html-format-drawer-function) (:html-format-headline-function nil nil org-html-format-headline-function) (:html-format-inlinetask-function nil nil org-html-format-inlinetask-function) (:html-home/up-format nil nil org-html-home/up-format) (:html-indent nil nil org-html-indent) (:html-infojs-options nil nil org-html-infojs-options) (:html-infojs-template nil nil org-html-infojs-template) (:html-inline-image-rules nil nil org-html-inline-image-rules) (:html-link-org-files-as-html nil nil org-html-link-org-files-as-html) (:html-mathjax-options nil nil org-html-mathjax-options) (:html-mathjax-template nil nil org-html-mathjax-template) (:html-metadata-timestamp-format nil nil org-html-metadata-timestamp-format) (:html-postamble-format nil nil org-html-postamble-format) (:html-preamble-format nil nil org-html-preamble-format) (:html-prefer-user-labels nil nil org-html-prefer-user-labels) (:html-self-link-headlines nil nil org-html-self-link-headlines) (:html-table-align-individual-fields nil nil org-html-table-align-individual-fields) (:html-table-caption-above nil nil org-html-table-caption-above) (:html-table-data-tags nil nil org-html-table-data-tags) (:html-table-header-tags nil nil org-html-table-header-tags) (:html-table-use-header-tags-for-first-column nil nil org-html-table-use-header-tags-for-first-column) (:html-tag-class-prefix nil nil org-html-tag-class-prefix) (:html-text-markup-alist nil nil org-html-text-markup-alist) (:html-todo-kwd-class-prefix nil nil org-html-todo-kwd-class-prefix) (:html-toplevel-hlevel nil nil org-html-toplevel-hlevel) (:html-use-infojs nil nil org-html-use-infojs) (:html-validation-link nil nil org-html-validation-link) (:html-viewport nil nil org-html-viewport) (:html-inline-images nil nil org-html-inline-images) (:html-table-attributes nil nil org-html-table-default-attributes) (:html-table-row-open-tag nil nil org-html-table-row-open-tag) (:html-table-row-close-tag nil nil org-html-table-row-close-tag) (:html-xml-declaration nil nil org-html-xml-declaration) (:html-wrap-src-lines nil nil org-html-wrap-src-lines) (:html-klipsify-src nil nil org-html-klipsify-src) (:html-klipse-css nil nil org-html-klipse-css) (:html-klipse-js nil nil org-html-klipse-js) (:html-klipse-selection-script nil nil org-html-klipse-selection-script) (:infojs-opt "INFOJS_OPT" nil nil) (:creator "CREATOR" nil org-html-creator-string) (:with-latex nil "tex" org-html-with-latex) (:latex-header "LATEX_HEADER" nil nil newline)) :filters ((:filter-options . org-html-infojs-install-script) (:filter-parse-tree . org-html-image-link-filter) (:filter-final-output . org-html-final-function)) :blocks nil :menu (104 "Export to HTML" ((72 "As HTML buffer" org-html-export-as-html) (104 "As HTML file" org-html-export-to-html) (111 "As HTML file and open" (lambda (a s v b) (if a (org-html-export-to-html t s v b) (org-open-file (org-html-export-to-html nil s v b)))))))) :translate-alist ((bold . org-html-bold) (center-block . org-html-center-block) (clock . org-html-clock) (code . org-html-code) (drawer . org-html-drawer) (dynamic-block . org-html-dynamic-block) (entity . org-html-entity) (example-block . org-html-example-block) (export-block . org-html-export-block) (export-snippet . org-html-export-snippet) (fixed-width . org-html-fixed-width) (footnote-reference . org-html-footnote-reference) (headline . org-html-headline) (horizontal-rule . org-html-horizontal-rule) (inline-src-block . org-html-inline-src-block) (inlinetask . org-html-inlinetask) (inner-template . org-html-inner-template) (italic . org-html-italic) (item . org-html-item) (keyword . org-html-keyword) (latex-environment . org-html-latex-environment) (latex-fragment . org-html-latex-fragment) (line-break . org-html-line-break) (link . org-html-link) (node-property . org-html-node-property) (paragraph . org-html-paragraph) (plain-list . org-html-plain-list) (plain-text . org-html-plain-text) (planning . org-html-planning) (property-drawer . org-html-property-drawer) (quote-block . org-html-quote-block) (radio-target . org-html-radio-target) (section . org-html-section) (special-block . org-html-special-block) (src-block . org-html-src-block) (statistics-cookie . org-html-statistics-cookie) (strike-through . org-html-strike-through) (subscript . org-html-subscript) (superscript . org-html-superscript) (table . org-html-table) (table-cell . org-html-table-cell) (table-row . org-html-table-row) (target . org-html-target) (template . org-html-template) (timestamp . org-html-timestamp) (underline . org-html-underline) (verbatim . org-html-verbatim) (verse-block . org-html-verse-block)) :exported-data # :input-buffer " *temp*" :input-file nil :html-doctype "xhtml-strict" :html-container "div" :html-content-class "content" :description nil :keywords nil :html-html5-fancy nil :html-link-use-abs-url nil :html-link-home "" :html-link-up "" :html-mathjax "" :html-equation-reference-format "\\eqref{%s}" :html-postamble auto :html-preamble t :html-head "" :html-head-extra "" :subtitle nil :html-head-include-default-style t :html-head-include-scripts nil :html-allow-name-attribute-in-anchors nil :html-divs ((preamble "div" "preamble") (content "div" "content") (postamble "div" "postamble")) :html-checkbox-type ascii :html-extension "html" :html-footnote-format "%s" :html-footnote-separator ", " :html-footnotes-section ") :html-format-headline-function org-html-format-headline-default-function :html-format-inlinetask-function org-html-format-inlinetask-default-function :html-home/up-format "" :html-indent nil :html-infojs-options ((path . "https://orgmode.org/org-info.js") (view . "info") (toc . :with-toc) (ftoc . "0") (tdepth . "max") (sdepth . "max") (mouse . "underline") (buttons . "0") (ltoc . "1") (up . :html-link-up) (home . :html-link-home)) :html-infojs-template "\n\n" :html-inline-image-rules (("file" . "\\(?:\\.\\(?:avif\\|gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("http" . "\\(?:\\.\\(?:avif\\|gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)") ("https" . "\\(?:\\.\\(?:avif\\|gif\\|jp\\(?:e?g\\)\\|png\\|svg\\|webp\\)\\)")) :html-link-org-files-as-html t :html-mathjax-options ((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js") (scale 1.0) (align "center") (font "mathjax-modern") (overflow "overflow") (tags "ams") (indent "0em") (multlinewidth "85%") (tagindent ".8em") (tagside "right")) :html-mathjax-template "\n\n" :html-metadata-timestamp-format "%Y-%m-%d %a %H:%M" :html-postamble-format (("en" "\n" . " ") :html-table-header-tags ("" . " ") :html-table-use-header-tags-for-first-column nil :html-tag-class-prefix "" :html-text-markup-alist ((bold . "%s") (code . "%s") (underline . "%s") (verbatim . "" :html-table-row-close-tag " " :html-xml-declaration (("html" . "") ("php" . "\"; ?>")) :html-wrap-src-lines nil :html-klipsify-src nil :html-klipse-css "https://storage.googleapis.com/app.klipse.tech/css/codemirror.css" :html-klipse-js "https://storage.googleapis.com/app.klipse.tech/plugin_prod/js/klipse_plugin.min.js" :html-klipse-selection-script "window.klipse_settings = {selector_eval_html: '.src-html',\n selector_eval_js: '.src-js',\n selector_eval_python_client: '.src-python',\n selector_eval_scheme: '.src-scheme',\n selector: '.src-clojure',\n selector_eval_ruby: '.src-ruby'};" :infojs-opt nil :creator "Emacs 30.2 (Org mode 9.7.11)" :with-latex t :latex-header nil :title (#("Installing GeneNetwork services with GNU Guix" 0 45 (:parent #148))) :date nil :author (#("unknown" 0 7 (:parent #152))) :email "unknown@genenetwork-development" :language "en" :select-tags ("export") :exclude-tags ("noexport") :headline-levels 3 :preserve-breaks nil :section-numbers nil :time-stamp-file t :with-archived-trees headline :with-author t :expand-links t :with-broken-links nil :with-clocks nil :with-creator nil :with-date t :with-drawers (not "LOGBOOK") :with-email nil :with-emphasize t :with-entities t :with-fixed-width t :with-footnotes t :with-inlinetasks t :with-planning nil :with-priority nil :with-properties nil :with-smart-quotes nil :with-special-strings t :with-special-rows nil :with-statistics-cookies t :with-sub-superscript t :with-toc nil :with-tables t :with-tags t :with-tasks t :with-timestamps t :with-title t :with-todo-keywords t :with-cite-processors t :cite-export (basic nil nil) :bibliography nil :filter-body nil :filter-bold nil :filter-babel-call nil :filter-center-block nil :filter-clock nil :filter-code nil :filter-diary-sexp nil :filter-drawer nil :filter-dynamic-block nil :filter-entity nil :filter-example-block nil :filter-export-block nil :filter-export-snippet nil :filter-final-output (org-html-final-function) :filter-fixed-width nil :filter-footnote-definition nil :filter-footnote-reference nil :filter-headline nil :filter-horizontal-rule nil :filter-inline-babel-call nil :filter-inline-src-block nil :filter-inlinetask nil :filter-italic nil :filter-item nil :filter-keyword nil :filter-latex-environment nil :filter-latex-fragment nil :filter-line-break nil :filter-link nil :filter-node-property nil :filter-options (org-html-infojs-install-script) :filter-paragraph nil :filter-parse-tree (org-html-image-link-filter) :filter-plain-list nil :filter-plain-text nil :filter-planning nil :filter-property-drawer nil :filter-quote-block nil :filter-radio-target nil :filter-section nil :filter-special-block nil :filter-src-block nil :filter-statistics-cookie nil :filter-strike-through nil :filter-subscript nil :filter-superscript nil :filter-table nil :filter-table-cell nil :filter-table-row nil :filter-target nil :filter-timestamp nil :filter-underline nil :filter-verbatim nil :filter-verse-block nil :ignore-list nil :parse-tree (org-data (:standard-properties [1 1 1 2040 2040 0 nil org-data nil nil nil 3 2040 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 57 57 0 nil first-section nil nil nil 1 57 nil # nil nil #344]) (keyword (:standard-properties [1 1 nil nil 57 1 nil top-comment nil nil nil nil nil nil # nil nil #347] :key "TITLE" :value "Installing GeneNetwork services with GNU Guix"))) (headline (:standard-properties [57 57 135 310 310 0 (:title) nil nil nil nil 137 308 1 # nil nil #344] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #348))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [135 135 135 310 310 0 nil section nil nil nil 135 310 nil # nil nil #348]) (plain-list (:standard-properties [135 135 135 309 310 1 nil planning nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #351] :type unordered) (item (:standard-properties [135 135 138 170 170 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #354] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [138 138 138 170 170 0 nil nil nil nil nil nil nil nil # nil nil #357]) (link (:standard-properties [138 nil 155 167 169 0 nil nil nil nil nil nil nil nil # nil nil #360] :type "custom-id" :type-explicit-p nil :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil) #("Introduction" 0 12 (:parent #363))) #("\n" 0 1 (:parent #360)))) (item (:standard-properties [170 170 173 215 215 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #354] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [173 173 173 215 215 0 nil nil nil nil nil nil nil nil # nil nil #358]) (link (:standard-properties [173 nil 195 212 214 0 nil nil nil nil nil nil nil nil # nil nil #361] :type "custom-id" :type-explicit-p nil :path "binary-deployment" :format bracket :raw-link "#binary-deployment" :application nil :search-option nil) #("Binary deployment" 0 17 (:parent #364))) #("\n" 0 1 (:parent #361)))) (item (:standard-properties [215 215 218 270 270 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #354] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [218 218 218 270 270 0 nil nil nil nil nil nil nil nil # nil nil #359]) (link (:standard-properties [218 nil 245 267 269 0 nil nil nil nil nil nil nil nil # nil nil #362] :type "custom-id" :type-explicit-p nil :path "from-source-deployment" :format bracket :raw-link "#from-source-deployment" :application nil :search-option nil) #("From source deployment" 0 22 (:parent #365))) #("\n" 0 1 (:parent #362)))) (item (:standard-properties [270 270 273 309 309 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #354] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [273 273 273 309 309 0 nil nil nil nil nil nil nil nil # nil nil #360]) (link (:standard-properties [273 nil 292 306 308 0 nil nil nil nil nil nil nil nil # nil nil #363] :type "custom-id" :type-explicit-p nil :path "create-archive" :format bracket :raw-link "#create-archive" :application nil :search-option nil) #("Create archive" 0 14 (:parent #366))) #("\n" 0 1 (:parent #363))))))) (headline (:standard-properties [310 310 326 557 557 0 (:title) nil nil nil nil 328 555 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #349))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [326 326 326 557 557 0 nil section nil nil nil 326 557 nil # nil nil #349]) (paragraph (:standard-properties [326 326 326 556 557 1 nil planning nil nil nil nil nil nil # nil nil #352]) #("Large system deployments tend to get very complex. In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #355)) (link (:standard-properties [479 nil 541 551 553 0 nil nil nil nil nil nil nil nil # nil nil #355] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #359))) #(").\n" 0 3 (:parent #355))))) (headline (:standard-properties [557 557 578 603 603 0 (:title) nil nil nil nil 580 601 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 19) t] :title (#("Binary deployment" 0 17 (:parent #350))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [578 578 578 603 603 0 nil section nil nil nil 578 603 nil # nil nil #350]) (paragraph (:standard-properties [578 578 578 602 603 1 nil planning nil nil nil nil nil nil # nil nil #353]) #("NYA (will go to README)\n" 0 24 (:parent #356))))) (headline (:standard-properties [603 603 629 1877 1877 0 (:title) nil nil nil nil 631 1875 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (:parent #351))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [629 629 629 1877 1877 0 nil section nil nil nil 629 1877 nil # nil nil #351]) (paragraph (:standard-properties [629 629 629 809 810 1 nil planning nil nil nil nil nil nil # nil nil #354]) #("GNU Guix allows for " 0 20 (:parent #357)) (link (:standard-properties [649 nil 718 741 744 1 nil nil nil nil nil nil nil nil # nil nil #357] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #361))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #357))) (src-block (:standard-properties [810 810 nil nil 1016 1 nil nil nil nil nil nil nil nil # nil nil #354] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [1016 1016 1016 1191 1192 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #359)) (link (:standard-properties [1072 nil 1177 1187 1189 0 nil nil nil nil nil nil nil nil # nil nil #359] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #363))) #(".\n" 0 2 (:parent #359))) (paragraph (:standard-properties [1192 1192 1192 1255 1256 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #360))) (fixed-width (:standard-properties [1256 1256 nil nil 1312 2 nil nil nil nil nil nil nil nil # nil nil #354] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [1312 1312 1312 1315 1316 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("So\n" 0 3 (:parent #362))) (paragraph (:standard-properties [1316 1316 1316 1702 1703 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("#+begin" 0 7 (:parent #363)) (subscript (:standard-properties [1323 nil 1324 1327 1328 1 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("src" 0 3 (:parent #367))) #("sh :lang bash\n#+begin" 0 23 (:parent #363)) (subscript (:standard-properties [1351 nil 1352 1355 1356 1 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #363)) (subscript (:standard-properties [1396 nil 1397 1404 1404 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #371))) (subscript (:standard-properties [1404 nil 1405 1409 1409 0 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("PATH" 0 4 (:parent #372))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #363)) (subscript (:standard-properties [1681 nil 1682 1685 1686 1 nil nil nil nil nil nil nil nil # nil nil #363] :use-brackets-p nil) #("src" 0 3 (:parent #374))) #("sh :lang bash\n" 0 16 (:parent #363))) (paragraph (:standard-properties [1703 1703 1703 1716 1717 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("Install with\n" 0 13 (:parent #364))) (paragraph (:standard-properties [1717 1717 1717 1876 1877 1 nil nil nil nil nil nil nil nil # nil nil #354]) #("#+begin" 0 7 (:parent #365)) (subscript (:standard-properties [1724 nil 1725 1728 1729 1 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #369))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #365)) (subscript (:standard-properties [1769 nil 1770 1777 1777 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #371))) (subscript (:standard-properties [1777 nil 1778 1782 1782 0 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("PATH" 0 4 (:parent #372))) #("=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2\n#+end" 0 73 (:parent #365)) (subscript (:standard-properties [1855 nil 1856 1859 1860 1 nil nil nil nil nil nil nil nil # nil nil #365] :use-brackets-p nil) #("src" 0 3 (:parent #374))) #("sh :lang bash\n" 0 16 (:parent #365))))) (headline (:standard-properties [1877 1877 1895 2040 2040 0 (:title) nil nil nil nil 1897 2038 1 # nil nil #344] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 16) t] :title (#("Create archive" 0 14 (:parent #352))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1895 1895 1895 2040 2040 0 nil section nil nil nil 1895 2040 nil # nil nil #352]) (fixed-width (:standard-properties [1895 1895 nil nil 2040 1 nil planning nil nil nil nil nil nil # nil nil #355] :value "env GUIX_PACKAGE_PATH=../../genenetwork/guix-bioinformatics/ ./pre-inst-env guix archive --export -r genenetwork2 > guix_gn2-2.0-9e9475053.nar"))))) :headline-offset 0 :headline-numbering nil :id-alist nil :citations nil :id-local-cache #))
#f(compiled-function (element) #)((link (:standard-properties [138 nil 155 167 169 0 nil nil nil nil nil nil nil nil # nil nil (paragraph (:standard-properties [138 138 138 170 170 0 nil nil nil nil nil nil nil nil # nil nil (item (:standard-properties [135 135 138 170 170 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) (plain-list (:standard-properties [135 135 135 309 310 1 nil planning nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) (section (:standard-properties [135 135 135 310 310 0 nil section nil nil nil 135 310 nil # nil nil (headline (:standard-properties [57 57 135 310 310 0 (:title) nil nil nil nil 137 308 1 # nil nil (org-data (:standard-properties [1 1 1 2040 2040 0 nil org-data nil nil nil 3 2040 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 57 57 0 nil first-section nil nil nil 1 57 nil # nil nil #30]) (keyword (:standard-properties [1 1 nil nil 57 1 nil top-comment nil nil nil nil nil nil # nil nil #33] :key "TITLE" :value "Installing GeneNetwork services with GNU Guix"))) #25 (headline (:standard-properties [310 310 326 557 557 0 (:title) nil nil nil nil 328 555 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [326 326 326 557 557 0 nil section nil nil nil 326 557 nil # nil nil #35]) (paragraph (:standard-properties [326 326 326 556 557 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Large system deployments tend to get very complex. In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #41)) (link (:standard-properties [479 nil 541 551 553 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #45))) #(").\n" 0 3 (:parent #41))))) (headline (:standard-properties [557 557 578 603 603 0 (:title) nil nil nil nil 580 601 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 19) t] :title (#("Binary deployment" 0 17 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [578 578 578 603 603 0 nil section nil nil nil 578 603 nil # nil nil #36]) (paragraph (:standard-properties [578 578 578 602 603 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("NYA (will go to README)\n" 0 24 (:parent #42))))) (headline (:standard-properties [603 603 629 1877 1877 0 (:title) nil nil nil nil 631 1875 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [629 629 629 1877 1877 0 nil section nil nil nil 629 1877 nil # nil nil #37]) (paragraph (:standard-properties [629 629 629 809 810 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("GNU Guix allows for " 0 20 (:parent #43)) (link (:standard-properties [649 nil 718 741 744 1 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #47))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #43))) (src-block (:standard-properties [810 810 nil nil 1016 1 nil nil nil nil nil nil nil nil # nil nil #40] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [1016 1016 1016 1191 1192 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #45)) (link (:standard-properties [1072 nil 1177 1187 1189 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #49))) #(".\n" 0 2 (:parent #45))) (paragraph (:standard-properties [1192 1192 1192 1255 1256 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #46))) (fixed-width (:standard-properties [1256 1256 nil nil 1312 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [1312 1312 1312 1315 1316 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("So\n" 0 3 (:parent #48))) (paragraph (:standard-properties [1316 1316 1316 1702 1703 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("#+begin" 0 7 (:parent #49)) (subscript (:standard-properties [1323 nil 1324 1327 1328 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("src" 0 3 (:parent #53))) #("sh :lang bash\n#+begin" 0 23 (:parent #49)) (subscript (:standard-properties [1351 nil 1352 1355 1356 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #49)) (subscript (:standard-properties [1396 nil 1397 1404 1404 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [1404 nil 1405 1409 1409 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #49)) (subscript (:standard-properties [1681 nil 1682 1685 1686 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("src" 0 3 (:parent #60))) #("sh :lang bash\n" 0 16 (:parent #49))) (paragraph (:standard-properties [1703 1703 1703 1716 1717 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Install with\n" 0 13 (:parent #50))) (paragraph (:standard-properties [1717 1717 1717 1876 1877 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("#+begin" 0 7 (:parent #51)) (subscript (:standard-properties [1724 nil 1725 1728 1729 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #51)) (subscript (:standard-properties [1769 nil 1770 1777 1777 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [1777 nil 1778 1782 1782 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2\n#+end" 0 73 (:parent #51)) (subscript (:standard-properties [1855 nil 1856 1859 1860 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("src" 0 3 (:parent #60))) #("sh :lang bash\n" 0 16 (:parent #51))))) (headline (:standard-properties [1877 1877 1895 2040 2040 0 (:title) nil nil nil nil 1897 2038 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 16) t] :title (#("Create archive" 0 14 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1895 1895 1895 2040 2040 0 nil section nil nil nil 1895 2040 nil # nil nil #38]) (fixed-width (:standard-properties [1895 1895 nil nil 2040 1 nil planning nil nil nil nil nil nil # nil nil #41] :value "env GUIX_PACKAGE_PATH=../../genenetwork/guix-bioinformatics/ ./pre-inst-env guix archive --export -r genenetwork2 > guix_gn2-2.0-9e9475053.nar")))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #25))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #20)]) #15)] :type unordered) #10 (item (:standard-properties [170 170 173 215 215 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #15] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [173 173 173 215 215 0 nil nil nil nil nil nil nil nil # nil nil #19]) (link (:standard-properties [173 nil 195 212 214 0 nil nil nil nil nil nil nil nil # nil nil #22] :type "custom-id" :type-explicit-p nil :path "binary-deployment" :format bracket :raw-link "#binary-deployment" :application nil :search-option nil) #("Binary deployment" 0 17 (:parent #25))) #("\n" 0 1 (:parent #22)))) (item (:standard-properties [215 215 218 270 270 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #15] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [218 218 218 270 270 0 nil nil nil nil nil nil nil nil # nil nil #20]) (link (:standard-properties [218 nil 245 267 269 0 nil nil nil nil nil nil nil nil # nil nil #23] :type "custom-id" :type-explicit-p nil :path "from-source-deployment" :format bracket :raw-link "#from-source-deployment" :application nil :search-option nil) #("From source deployment" 0 22 (:parent #26))) #("\n" 0 1 (:parent #23)))) (item (:standard-properties [270 270 273 309 309 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #15] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [273 273 273 309 309 0 nil nil nil nil nil nil nil nil # nil nil #21]) (link (:standard-properties [273 nil 292 306 308 0 nil nil nil nil nil nil nil nil # nil nil #24] :type "custom-id" :type-explicit-p nil :path "create-archive" :format bracket :raw-link "#create-archive" :application nil :search-option nil) #("Create archive" 0 14 (:parent #27))) #("\n" 0 1 (:parent #24)))))] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) #5)]) #0 #("\n" 0 1 (:parent #5)))] :type "custom-id" :type-explicit-p nil :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil) #("Introduction" 0 12 (:parent #0))))
mapconcat(#f(compiled-function (element) #) ((link (:standard-properties [138 nil 155 167 169 0 nil nil nil nil nil nil nil nil # nil nil (paragraph (:standard-properties [138 138 138 170 170 0 nil nil nil nil nil nil nil nil # nil nil (item (:standard-properties [135 135 138 170 170 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) (plain-list (:standard-properties [135 135 135 309 310 1 nil planning nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) (section (:standard-properties [135 135 135 310 310 0 nil section nil nil nil 135 310 nil # nil nil (headline (:standard-properties [57 57 135 310 310 0 (:title) nil nil nil nil 137 308 1 # nil nil (org-data (:standard-properties [1 1 1 2040 2040 0 nil org-data nil nil nil 3 2040 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 57 57 0 nil first-section nil nil nil 1 57 nil # nil nil #31]) (keyword (:standard-properties [1 1 nil nil 57 1 nil top-comment nil nil nil nil nil nil # nil nil #34] :key "TITLE" :value "Installing GeneNetwork services with GNU Guix"))) #26 (headline (:standard-properties [310 310 326 557 557 0 (:title) nil nil nil nil 328 555 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [326 326 326 557 557 0 nil section nil nil nil 326 557 nil # nil nil #36]) (paragraph (:standard-properties [326 326 326 556 557 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("Large system deployments tend to get very complex. In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #42)) (link (:standard-properties [479 nil 541 551 553 0 nil nil nil nil nil nil nil nil # nil nil #42] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #46))) #(").\n" 0 3 (:parent #42))))) (headline (:standard-properties [557 557 578 603 603 0 (:title) nil nil nil nil 580 601 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 19) t] :title (#("Binary deployment" 0 17 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [578 578 578 603 603 0 nil section nil nil nil 578 603 nil # nil nil #37]) (paragraph (:standard-properties [578 578 578 602 603 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("NYA (will go to README)\n" 0 24 (:parent #43))))) (headline (:standard-properties [603 603 629 1877 1877 0 (:title) nil nil nil nil 631 1875 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [629 629 629 1877 1877 0 nil section nil nil nil 629 1877 nil # nil nil #38]) (paragraph (:standard-properties [629 629 629 809 810 1 nil planning nil nil nil nil nil nil # nil nil #41]) #("GNU Guix allows for " 0 20 (:parent #44)) (link (:standard-properties [649 nil 718 741 744 1 nil nil nil nil nil nil nil nil # nil nil #44] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #48))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #44))) (src-block (:standard-properties [810 810 nil nil 1016 1 nil nil nil nil nil nil nil nil # nil nil #41] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [1016 1016 1016 1191 1192 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #46)) (link (:standard-properties [1072 nil 1177 1187 1189 0 nil nil nil nil nil nil nil nil # nil nil #46] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #50))) #(".\n" 0 2 (:parent #46))) (paragraph (:standard-properties [1192 1192 1192 1255 1256 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #47))) (fixed-width (:standard-properties [1256 1256 nil nil 1312 2 nil nil nil nil nil nil nil nil # nil nil #41] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [1312 1312 1312 1315 1316 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("So\n" 0 3 (:parent #49))) (paragraph (:standard-properties [1316 1316 1316 1702 1703 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("#+begin" 0 7 (:parent #50)) (subscript (:standard-properties [1323 nil 1324 1327 1328 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("src" 0 3 (:parent #54))) #("sh :lang bash\n#+begin" 0 23 (:parent #50)) (subscript (:standard-properties [1351 nil 1352 1355 1356 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("src" 0 3 (:parent #56))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #50)) (subscript (:standard-properties [1396 nil 1397 1404 1404 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #58))) (subscript (:standard-properties [1404 nil 1405 1409 1409 0 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("PATH" 0 4 (:parent #59))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #50)) (subscript (:standard-properties [1681 nil 1682 1685 1686 1 nil nil nil nil nil nil nil nil # nil nil #50] :use-brackets-p nil) #("src" 0 3 (:parent #61))) #("sh :lang bash\n" 0 16 (:parent #50))) (paragraph (:standard-properties [1703 1703 1703 1716 1717 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("Install with\n" 0 13 (:parent #51))) (paragraph (:standard-properties [1717 1717 1717 1876 1877 1 nil nil nil nil nil nil nil nil # nil nil #41]) #("#+begin" 0 7 (:parent #52)) (subscript (:standard-properties [1724 nil 1725 1728 1729 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("src" 0 3 (:parent #56))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #52)) (subscript (:standard-properties [1769 nil 1770 1777 1777 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #58))) (subscript (:standard-properties [1777 nil 1778 1782 1782 0 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("PATH" 0 4 (:parent #59))) #("=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2\n#+end" 0 73 (:parent #52)) (subscript (:standard-properties [1855 nil 1856 1859 1860 1 nil nil nil nil nil nil nil nil # nil nil #52] :use-brackets-p nil) #("src" 0 3 (:parent #61))) #("sh :lang bash\n" 0 16 (:parent #52))))) (headline (:standard-properties [1877 1877 1895 2040 2040 0 (:title) nil nil nil nil 1897 2038 1 # nil nil #31] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 16) t] :title (#("Create archive" 0 14 (:parent #39))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1895 1895 1895 2040 2040 0 nil section nil nil nil 1895 2040 nil # nil nil #39]) (fixed-width (:standard-properties [1895 1895 nil nil 2040 1 nil planning nil nil nil nil nil nil # nil nil #42] :value "env GUIX_PACKAGE_PATH=../../genenetwork/guix-bioinformatics/ ./pre-inst-env guix archive --export -r genenetwork2 > guix_gn2-2.0-9e9475053.nar")))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #26))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #21)]) #16)] :type unordered) #11 (item (:standard-properties [170 170 173 215 215 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #16] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [173 173 173 215 215 0 nil nil nil nil nil nil nil nil # nil nil #20]) (link (:standard-properties [173 nil 195 212 214 0 nil nil nil nil nil nil nil nil # nil nil #23] :type "custom-id" :type-explicit-p nil :path "binary-deployment" :format bracket :raw-link "#binary-deployment" :application nil :search-option nil) #("Binary deployment" 0 17 (:parent #26))) #("\n" 0 1 (:parent #23)))) (item (:standard-properties [215 215 218 270 270 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #16] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [218 218 218 270 270 0 nil nil nil nil nil nil nil nil # nil nil #21]) (link (:standard-properties [218 nil 245 267 269 0 nil nil nil nil nil nil nil nil # nil nil #24] :type "custom-id" :type-explicit-p nil :path "from-source-deployment" :format bracket :raw-link "#from-source-deployment" :application nil :search-option nil) #("From source deployment" 0 22 (:parent #27))) #("\n" 0 1 (:parent #24)))) (item (:standard-properties [270 270 273 309 309 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #16] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [273 273 273 309 309 0 nil nil nil nil nil nil nil nil # nil nil #22]) (link (:standard-properties [273 nil 292 306 308 0 nil nil nil nil nil nil nil nil # nil nil #25] :type "custom-id" :type-explicit-p nil :path "create-archive" :format bracket :raw-link "#create-archive" :application nil :search-option nil) #("Create archive" 0 14 (:parent #28))) #("\n" 0 1 (:parent #25)))))] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) #6)]) . #0)] :type "custom-id" :type-explicit-p nil :path "introduction" :format bracket :raw-link "#introduction" :application nil :search-option nil) #("Introduction" 0 12 (:parent #1))) #("\n" 0 1 (:parent (paragraph (:standard-properties [138 138 138 170 170 0 nil nil nil nil nil nil nil nil # nil nil (item (:standard-properties [135 135 138 170 170 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) (plain-list (:standard-properties [135 135 135 309 310 1 nil planning nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) (section (:standard-properties [135 135 135 310 310 0 nil section nil nil nil 135 310 nil # nil nil (headline (:standard-properties [57 57 135 310 310 0 (:title) nil nil nil nil 137 308 1 # nil nil (org-data (:standard-properties [1 1 1 2040 2040 0 nil org-data nil nil nil 3 2040 nil # nil nil nil] :path nil :CATEGORY nil) (section (:standard-properties [1 1 1 57 57 0 nil first-section nil nil nil 1 57 nil # nil nil #30]) (keyword (:standard-properties [1 1 nil nil 57 1 nil top-comment nil nil nil nil nil nil # nil nil #33] :key "TITLE" :value "Installing GeneNetwork services with GNU Guix"))) #25 (headline (:standard-properties [310 310 326 557 557 0 (:title) nil nil nil nil 328 555 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 14) t] :title (#("Introduction" 0 12 (:parent #35))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [326 326 326 557 557 0 nil section nil nil nil 326 557 nil # nil nil #35]) (paragraph (:standard-properties [326 326 326 556 557 1 nil planning nil nil nil nil nil nil # nil nil #38]) #("Large system deployments tend to get very complex. In this document we\nexplain the GeneNetwork deployment system which is based on GNU Guix\n(see Pjotr's " 0 153 (:parent #41)) (link (:standard-properties [479 nil 541 551 553 0 nil nil nil nil nil nil nil nil # nil nil #41] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/README.md" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/README.md" :application nil :search-option nil) #("Guix-notes" 0 10 (:parent #45))) #(").\n" 0 3 (:parent #41))))) (headline (:standard-properties [557 557 578 603 603 0 (:title) nil nil nil nil 580 601 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 19) t] :title (#("Binary deployment" 0 17 (:parent #36))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [578 578 578 603 603 0 nil section nil nil nil 578 603 nil # nil nil #36]) (paragraph (:standard-properties [578 578 578 602 603 1 nil planning nil nil nil nil nil nil # nil nil #39]) #("NYA (will go to README)\n" 0 24 (:parent #42))))) (headline (:standard-properties [603 603 629 1877 1877 0 (:title) nil nil nil nil 631 1875 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 24) t] :title (#("From source deployment" 0 22 (:parent #37))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [629 629 629 1877 1877 0 nil section nil nil nil 629 1877 nil # nil nil #37]) (paragraph (:standard-properties [629 629 629 809 810 1 nil planning nil nil nil nil nil nil # nil nil #40]) #("GNU Guix allows for " 0 20 (:parent #43)) (link (:standard-properties [649 nil 718 741 744 1 nil nil nil nil nil nil nil nil # nil nil #43] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org" :application nil :search-option nil) #("reproducible deployment" 0 23 (:parent #47))) #("based on a checked out\nGuix repository - use gn-stable for that:\n" 0 65 (:parent #43))) (src-block (:standard-properties [810 810 nil nil 1016 1 nil nil nil nil nil nil nil nil # nil nil #40] :language "sh" :switches nil :parameters ":lang bash" :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value [org-element-deferred org-element--unescape-substring (26 195) t])) (paragraph (:standard-properties [1016 1016 1016 1191 1192 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Next build guix (and run) following the instructions in " 0 56 (:parent #45)) (link (:standard-properties [1072 nil 1177 1187 1189 0 nil nil nil nil nil nil nil nil # nil nil #45] :type "https" :type-explicit-p t :path "//github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :format bracket :raw-link "https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix" :application nil :search-option nil) #("guix-notes" 0 10 (:parent #49))) #(".\n" 0 2 (:parent #45))) (paragraph (:standard-properties [1192 1192 1192 1255 1256 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Once that is done we can add the guix-bioinformatics path with\n" 0 63 (:parent #46))) (fixed-width (:standard-properties [1256 1256 nil nil 1312 2 nil nil nil nil nil nil nil nil # nil nil #40] :value "env GUIX_PACKAGE_PATH=../guix-bioinformatics command")) (paragraph (:standard-properties [1312 1312 1312 1315 1316 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("So\n" 0 3 (:parent #48))) (paragraph (:standard-properties [1316 1316 1316 1702 1703 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("#+begin" 0 7 (:parent #49)) (subscript (:standard-properties [1323 nil 1324 1327 1328 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("src" 0 3 (:parent #53))) #("sh :lang bash\n#+begin" 0 23 (:parent #49)) (subscript (:standard-properties [1351 nil 1352 1355 1356 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #49)) (subscript (:standard-properties [1396 nil 1397 1404 1404 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [1404 nil 1405 1409 1409 0 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork\ngenenetwork1 1.0-d622c803b out ../guix-bioinformatics/gn/packages/bioinformatics.scm:163:2\ngenenetwork2 2.0-9e9475053 out ../guix-bioinformatics/gn/packages/bioinformatics.scm:215:2\n#+end" 0 272 (:parent #49)) (subscript (:standard-properties [1681 nil 1682 1685 1686 1 nil nil nil nil nil nil nil nil # nil nil #49] :use-brackets-p nil) #("src" 0 3 (:parent #60))) #("sh :lang bash\n" 0 16 (:parent #49))) (paragraph (:standard-properties [1703 1703 1703 1716 1717 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("Install with\n" 0 13 (:parent #50))) (paragraph (:standard-properties [1717 1717 1717 1876 1877 1 nil nil nil nil nil nil nil nil # nil nil #40]) #("#+begin" 0 7 (:parent #51)) (subscript (:standard-properties [1724 nil 1725 1728 1729 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("src" 0 3 (:parent #55))) #("sh :lang bash\ngn-stable-guix$ env GUIX" 0 40 (:parent #51)) (subscript (:standard-properties [1769 nil 1770 1777 1777 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PACKAGE" 0 7 (:parent #57))) (subscript (:standard-properties [1777 nil 1778 1782 1782 0 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("PATH" 0 4 (:parent #58))) #("=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2\n#+end" 0 73 (:parent #51)) (subscript (:standard-properties [1855 nil 1856 1859 1860 1 nil nil nil nil nil nil nil nil # nil nil #51] :use-brackets-p nil) #("src" 0 3 (:parent #60))) #("sh :lang bash\n" 0 16 (:parent #51))))) (headline (:standard-properties [1877 1877 1895 2040 2040 0 (:title) nil nil nil nil 1897 2038 1 # nil nil #30] :pre-blank 1 :raw-value [org-element-deferred org-element--headline-raw-value (2 16) t] :title (#("Create archive" 0 14 (:parent #38))) :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) (section (:standard-properties [1895 1895 1895 2040 2040 0 nil section nil nil nil 1895 2040 nil # nil nil #38]) (fixed-width (:standard-properties [1895 1895 nil nil 2040 1 nil planning nil nil nil nil nil nil # nil nil #41] :value "env GUIX_PACKAGE_PATH=../../genenetwork/guix-bioinformatics/ ./pre-inst-env guix archive --export -r genenetwork2 > guix_gn2-2.0-9e9475053.nar")))))] :pre-blank 0 :raw-value "Table of Contents" :title (#("Table of Contents" 0 17 (:parent #25))) :level 1 :priority nil :tags ("TOC") :todo-keyword nil :todo-type nil :footnote-section-p [org-element-deferred org-element--headline-footnote-section-p nil nil] :archivedp [org-element-deferred org-element--headline-archivedp nil nil] :commentedp nil) #20)]) #15)] :type unordered) #10 (item (:standard-properties [170 170 173 215 215 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #15] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [173 173 173 215 215 0 nil nil nil nil nil nil nil nil # nil nil #19]) (link (:standard-properties [173 nil 195 212 214 0 nil nil nil nil nil nil nil nil # nil nil #22] :type "custom-id" :type-explicit-p nil :path "binary-deployment" :format bracket :raw-link "#binary-deployment" :application nil :search-option nil) #("Binary deployment" 0 17 (:parent #25))) #("\n" 0 1 (:parent #22)))) (item (:standard-properties [215 215 218 270 270 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #15] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [218 218 218 270 270 0 nil nil nil nil nil nil nil nil # nil nil #20]) (link (:standard-properties [218 nil 245 267 269 0 nil nil nil nil nil nil nil nil # nil nil #23] :type "custom-id" :type-explicit-p nil :path "from-source-deployment" :format bracket :raw-link "#from-source-deployment" :application nil :search-option nil) #("From source deployment" 0 22 (:parent #26))) #("\n" 0 1 (:parent #23)))) (item (:standard-properties [270 270 273 309 309 0 (:tag) item nil nil nil nil nil nil # nil ((135 1 "- " nil nil nil 170) (170 1 "- " nil nil nil 215) (215 1 "- " nil nil nil 270) (270 1 "- " nil nil nil 309)) #15] :bullet "- " :checkbox nil :counter nil :pre-blank 0 :tag nil) (paragraph (:standard-properties [273 273 273 309 309 0 nil nil nil nil nil nil nil nil #
\n
" :html-format-drawer-function #f(compiled-function (name contents) #%s:
\n\n%s\n
\nDate: %d
\n%c
\n%v
")) :html-preamble-format (("en" "")) :html-prefer-user-labels nil :html-self-link-headlines nil :html-table-align-individual-fields t :html-table-caption-above t :html-table-data-tags ("%s") (italic . "%s") (strike-through . "%s")) :html-todo-kwd-class-prefix "" :html-toplevel-hlevel 2 :html-use-infojs when-configured :html-validation-link "Validate" :html-viewport ((width "device-width") (initial-scale "1") (minimum-scale "") (maximum-scale "") (user-scalable "")) :html-inline-images t :html-table-attributes (:border "2" :cellspacing "0" :cellpadding "6" :rules "groups" :frame "hsides") :html-table-row-open-tag "