Merge branch 'main' of github.com:bsurc/container into main

sagedale/Makefile

@@ -0,0 +1,11 @@
+GIT_REV = $(shell git rev-parse --short=16 HEAD)
+sagedale.sif: apptainer guix.out
+	apptainer build -F --fakeroot --build-arg GIT_REV=$(GIT_REV) --build-arg GUIX_SQUASHFS=$$(tail -1 guix.out) sagedale.sif apptainer
+
+guix.out: channels.scm manifest.scm
+	guix time-machine -C channels.scm -- pack -f squashfs -m manifest.scm | tee guix.out
+
+.PHONY: clean
+clean:
+	rm -f *.sif
+	rm -f guix.out

sagedale/apptainer

@@ -0,0 +1,16 @@
+Bootstrap: localimage
+From: {{GUIX_SQUASHFS}}
+
+%files
+test.R /
+
+%post
+Rscript -e "devtools::install_github('GuillemSalazar/FastaUtils')"
+
+%test
+
+Rscript /test.R
+
+%labels
+author Kyle Shannon <[email protected]>
+github.com/bsurc/container git rev={{GIT_REV}}

sagedale/channels.scm

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+(list (channel
+        (name 'guix-cran)
+        (url "https://github.com/guix-science/guix-cran.git")
+        (branch "master")
+        (commit
+          "1304d8475452c995bf9da10ad242607f3791385e"))
+      (channel
+        (name 'guix-bioc)
+        (url "https://github.com/guix-science/guix-bioc.git")
+        (branch "master")
+        (commit
+          "e868814ccd7f5e6eefd726818899aa84c0c9d6ea"))
+      (channel
+        (name 'guix-hpc)
+        (url "https://gitlab.inria.fr/guix-hpc/guix-hpc.git")
+        (branch "master")
+        (commit
+          "f002aad7b66cd215b6a1720c48f08ed73f2661d5"))
+      (channel
+        (name 'guix-science)
+        (url "https://github.com/guix-science/guix-science.git")
+        (branch "master")
+        (commit
+          "f85279b8aeac3cc3e6e2aec866841c722c5663fe")
+        (introduction
+          (make-channel-introduction
+            "b1fe5aaff3ab48e798a4cce02f0212bc91f423dc"
+            (openpgp-fingerprint
+              "CA4F 8CF4 37D7 478F DA05  5FD4 4213 7701 1A37 8446"))))
+      (channel
+        (name 'guix)
+        (url "https://git.savannah.gnu.org/git/guix.git")
+        (branch "master")
+        (commit
+          "29987db3809bbda16762ecb349142be6cf71a0af")
+        (introduction
+          (make-channel-introduction
+            "9edb3f66fd807b096b48283debdcddccfea34bad"
+            (openpgp-fingerprint
+              "BBB0 2DDF 2CEA F6A8 0D1D  E643 A2A0 6DF2 A33A 54FA")))))

sagedale/manifest.scm

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+(specifications->manifest (list
+                            ;; base packages
+                            "bash-minimal"
+                            "glibc-locales"
+                            "nss-certs"
+                            ;; Common command line tools lest the container is too empty.
+                            "coreutils"
+                            "grep"
+                            "which"
+                            "wget"
+                            "sed"
+                            ;; Toolchain and common libraries for "install.packages"
+                            "gcc-toolchain@10"
+                            "gfortran-toolchain"
+                            "gawk"
+                            "tar"
+                            "gzip"
+                            "unzip"
+                            "make"
+                            "cmake"
+                            "pkg-config"
+                            "cairo"
+                            "libxt"
+                            "openssl"
+                            "curl"
+                            "zlib"
+                            ;; r stuff
+                            "r"
+                            "r-ape"
+                            "r-biostrings"
+                            "r-devtools"
+                            "r-dplyr"
+                            ;; "r-fastautils"
+                            "r-orfik"
+                            "r-readr"
+                            "r-tidyr"
+                            "r-rblast"
+                            "r-seqinr"
+                            "r-stringr"
+                          ))

sagedale/test.R

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+list.of.packages <- c("ape",
+                      "Biostrings",
+                      "dplyr",
+                      "FastaUtils",
+                      "ORFik",
+                      "readr",
+                      "tidyr",
+                      "rBLAST",
+                      "seqinr",
+                      "stringr")
+
+lapply(list.of.packages, require, character.only = TRUE)