"r-cran-roxygen2",
"r-cran-xml",
"sudo",
+ "uuid-dev",
"wget",
"xvfb",
)
+ if dev || test {
+ pkgs = append(pkgs,
+ "squashfs-tools", // for singularity
+ )
+ }
switch {
case osv.Debian && osv.Major >= 10:
pkgs = append(pkgs, "libcurl4")
}
if !prod {
- goversion := "1.16.3"
+ goversion := "1.17.1"
if havegoversion, err := exec.Command("/usr/local/bin/go", "version").CombinedOutput(); err == nil && bytes.HasPrefix(havegoversion, []byte("go version go"+goversion+" ")) {
logger.Print("go " + goversion + " already installed")
} else {
err = inst.runBash(`
cd /tmp
+rm -rf /var/lib/arvados/go/
wget --progress=dot:giga -O- https://storage.googleapis.com/golang/go`+goversion+`.linux-amd64.tar.gz | tar -C /var/lib/arvados -xzf -
ln -sf /var/lib/arvados/go/bin/* /usr/local/bin/
`, stdout, stderr)
}
}
- nodejsversion := "v10.23.1"
+ nodejsversion := "v12.22.2"
if havenodejsversion, err := exec.Command("/usr/local/bin/node", "--version").CombinedOutput(); err == nil && string(havenodejsversion) == nodejsversion+"\n" {
logger.Print("nodejs " + nodejsversion + " already installed")
} else {
}
}
+ singularityversion := "3.7.4"
+ if havesingularityversion, err := exec.Command("/var/lib/arvados/bin/singularity", "--version").CombinedOutput(); err == nil && strings.Contains(string(havesingularityversion), singularityversion) {
+ logger.Print("singularity " + singularityversion + " already installed")
+ } else if dev || test {
+ err = inst.runBash(`
+S=`+singularityversion+`
+tmp=/var/lib/arvados/tmp/singularity
+trap "rm -r ${tmp}" ERR EXIT
+cd /var/lib/arvados/tmp
+git clone https://github.com/sylabs/singularity
+cd singularity
+git checkout v${S}
+./mconfig --prefix=/var/lib/arvados
+make -C ./builddir
+make -C ./builddir install
+`, stdout, stderr)
+ if err != nil {
+ return 1
+ }
+ }
+
// The entry in /etc/locale.gen is "en_US.UTF-8"; once
// it's installed, locale -a reports it as
// "en_US.utf8".
{"mkdir", "-p", "log", "tmp", ".bundle", "/var/www/.gem", "/var/www/.bundle", "/var/www/.passenger"},
{"touch", "log/production.log"},
{"chown", "-R", "--from=root", "www-data:www-data", "/var/www/.gem", "/var/www/.bundle", "/var/www/.passenger", "log", "tmp", ".bundle", "Gemfile.lock", "config.ru", "config/environment.rb"},
- {"sudo", "-u", "www-data", "/var/lib/arvados/bin/gem", "install", "--user", "--conservative", "--no-document", "bundler:1.16.6", "bundler:1.17.3", "bundler:2.0.2"},
+ {"sudo", "-u", "www-data", "/var/lib/arvados/bin/gem", "install", "--user", "--conservative", "--no-document", "bundler:2.2.19"},
{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "install", "--deployment", "--jobs", "8", "--path", "/var/www/.gem"},
{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "build-native-support"},
{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "install-standalone-runtime"},