marvin: init at 19.1.0 #53839

fusion809 · 2019-01-12T12:06:24Z

Motivation for this change

The Marvin Suite is one of the finest skeletal structure drawing programs that is available free of cost to the end user. There are some features one must pay for, but most of them are advanced features that many users, like myself, don't really care about. Here's a screenshot showing it running, opened to a molecule of clozapine:

. I have added myself to the maintainers list, as this package, of course, needs a maintainer.

Things done

Area that could do with some improvement

Line 9 of the default.nix file could do with some improvement. Namely, if anyone knows a way I could let the nix file determine the version 19.1 from the full version 19.1.0, and use it in the URL, it'd be much appreciated :). I've tried using ${version%.?} and sadly, it merely caused Nix to give the error message:

error: syntax error, unexpected $undefined, expecting '}', at /home/fusion809/GitHub/mine/packaging/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix:9:77

fusion809 · 2019-01-12T12:13:19Z

Ticking the "other Linux distributions" box as I have now tried it on Arch Linux and it ran fine.

symphorien · 2019-01-12T13:04:34Z

pkgs/applications/science/chemistry/marvin/default.nix

+    mkdir $out/share/pixmaps
+    mkdir $out/bin
+    ln -sf $out/opt/chemaxon/marvinsuite/bin/msketch $out/bin/msketch
+    ln -sf $out/opt/chemaxon/marvinsuite/bin/mview $out/bin/mview


This does not work in an empty PATH.

PATH= $buildInputs/bin/mview /nix/store/jb299sb3abjqfh4zm7qpkd6ir0jl8jfc-marvin-19.1.0/bin/mview: line 362: basename: No such file or directory /nix/store/jb299sb3abjqfh4zm7qpkd6ir0jl8jfc-marvin-19.1.0/bin/mview: line 363: dirname: No such file or directory /nix/store/jb299sb3abjqfh4zm7qpkd6ir0jl8jfc-marvin-19.1.0/bin/mview: line 378: dirname: No such file or directory /nix/store/jb299sb3abjqfh4zm7qpkd6ir0jl8jfc-marvin-19.1.0/bin/mview: line 379: basename: No such file or directory No suitable Java Virtual Machine could be found on your system. The version of the JVM must be at least 1.8. Please define INSTALL4J_JAVA_HOME to point to a suitable JVM.

It would be preferable to wrap these executables with the jre (and coreutils apparently). random example:

nixpkgs/pkgs/applications/audio/abcde/default.nix

Lines 38 to 43 in b07e156

wrapProgram "$out/bin/$cmd" \

--prefix PERL5LIB : "$PERL5LIB" \

--prefix PATH ":" ${stdenv.lib.makeBinPath [

"$out" which libcdio-paranoia cddiscid wget

vorbis-tools id3v2 eyeD3 lame flac glyr

]}

Or if running a jar is enough:

nixpkgs/pkgs/applications/graphics/astah-community/default.nix

Lines 52 to 53 in b07e156

makeWrapper ${jre}/bin/java $out/bin/astah \

--add-flags "-jar $out/share/astah/astah-community.jar"

Thanks, although I must admit I'm a Nix beginner and Marvin has a whole directory of Java .jar files it uses, so your second suggestion (which I am able to follow) may not be applicable. Here's the contents of opt/chemaxon/marvinsuite: https://gist.github.com/78dcbe723995f9ab858f85db599c52f6. msketch has these contents: https://paste2.org/kEd9zFtL. It seems to be a shell wrapper in itself.

The executing command, when the variables are expanded, is incredibly complex, e.g. here is what it is when I've extracted it to a local directory at /home/fusion809/Programs/Deb/marvin: https://gist.github.com/fusion809/188669fd39c100a2cfadc42c72774fb4.

Oh thank goodness, I figured it out! Just had to find the docs for makeWrapper.

It still does not work for me in an empty PATH.

[nix-shell:~/.cache/nix-review/pr-53839]$ PATH= $buildInputs/bin/mview /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 362: basename: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 363: dirname: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 378: dirname: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 379: basename: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 66: expr: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 67: expr: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 81: awk: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 82: rm: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 83: mv: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 85: sed: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 88: chmod: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 66: expr: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 67: expr: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 81: awk: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 82: rm: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 83: mv: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 85: sed: No such file or directory /nix/store/vs9h3hws3slbrliryxi80abmf48dws4j-marvin-19.1.0/opt/chemaxon/marvinsuite/bin/mview: line 88: chmod: No such file or directory No suitable Java Virtual Machine could be found on your system. The version of the JVM must be at least 1.8. Please define INSTALL4J_JAVA_HOME to point to a suitable JVM.

You probably need to add something like --prefix PATH : ${makeBinPath [ coreutils awk sed ]}.
And the INSTALL4J_JAVA_HOME thing does not seem to work.
By the way, I find strange that a startup wrapper needs rm...

makeBinPath is in lib

Replacing makeBinPath with stdenv.lib.makeBinPath makes the build fail, with the error:

error: undefined variable 'coreutils' at /data/GitHub/mine/packaging/nixpkgs.marvin-pr/pkgs/applications/science/chemistry/marvin/default.nix:21:142

Sorry, I'm sure these are real stupid concerns, but I'm a beginner and I do not know why this is happening.

coreutils needs to be added to the arguments in the first line.

Thank you, I do believe I have fixed it. I tested with an empty PATH and it launched.

symphorien · 2019-01-12T13:07:38Z

pkgs/applications/science/chemistry/marvin/default.nix

+  buildInputs = [ dpkg makeWrapper ];
+  unpackPhase = ''
+    mkdir pkg/opt -p
+    dpkg-deb -x $src pkg/opt


you can directly unpack to $out/opt if you wish so.

Thanks, done in 1e14e08.

fusion809 · 2019-01-12T16:07:26Z

In my last commit 355f8d8, I added extra wrappers to $out/bin, for all executables in $out/opt/chemaxon/marvinsuite, so:

bin/cxcalc
bin/cxtrain
bin/evaluate
bin/molconvert
bin/msketch
bin/mview
LicenseManager
MarvinSketch
MarvinView

I also created a desktop config file for the ChemAxon License Manager.

symphorien · 2019-01-12T16:42:49Z

pkgs/applications/science/chemistry/marvin/default.nix

+    makeWrapper $out/opt/chemaxon/marvinsuite/bin/evaluate $out/bin/mview --set INSTALL4J_JAVA_HOME "${jre}"
+    makeWrapper $out/opt/chemaxon/marvinsuite/bin/molconvert $out/bin/mview --set INSTALL4J_JAVA_HOME "${jre}"
+    makeWrapper $out/opt/chemaxon/marvinsuite/bin/msketch $out/bin/msketch --set INSTALL4J_JAVA_HOME "${jre}"
+    makeWrapper $out/opt/chemaxon/marvinsuite/bin/mview $out/bin/mview --set INSTALL4J_JAVA_HOME "${jre}"


Nit: You can probably write a loop like

for i in cxcalc cxtrain etc; do makeWrapper $out/opt/chemaxon/marvinsuite/bin/$i $out/bin/$i --set INSTALL4J_JAVA_HOME "${jre}"; done

Done in 1cdba3e048c.

@msteen

Also adding myself (fusion809) as a maintainer. The marvin Nix file in this commit is largely thanks to @msteen.

fusion809 changed the title ~~marvin: init at 19.1~~ marvin: init at 19.1.0 Jan 12, 2019

GrahamcOfBorg added 8.has: package (new) This PR adds a new package 10.rebuild-darwin: 0 This PR does not cause any packages to rebuild on Darwin 10.rebuild-linux: 1-10 labels Jan 12, 2019

symphorien reviewed Jan 12, 2019

View reviewed changes

fusion809 force-pushed the marvin branch 4 times, most recently from 2be61d3 to 355f8d8 Compare January 12, 2019 15:58

symphorien reviewed Jan 12, 2019

View reviewed changes

fusion809 force-pushed the marvin branch 2 times, most recently from 1cdba3e to f6bb31a Compare January 12, 2019 18:12

symphorien approved these changes Jan 12, 2019

View reviewed changes

fusion809 force-pushed the marvin branch from f6bb31a to 2b68d08 Compare January 14, 2019 04:08

marvin: init at 19.1.0

6be5e67

Also adding myself (fusion809) as a maintainer. The marvin Nix file in this commit is largely thanks to @msteen.

fusion809 force-pushed the marvin branch from 2b68d08 to 6be5e67 Compare January 14, 2019 14:24

veprbl merged commit 0f3758b into NixOS:master Jan 19, 2019

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marvin: init at 19.1.0 #53839

marvin: init at 19.1.0 #53839

fusion809 commented Jan 12, 2019 •

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symphorien Jan 12, 2019

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fusion809 Jan 12, 2019

	wrapProgram "$out/bin/$cmd" \
	--prefix PERL5LIB : "$PERL5LIB" \
	--prefix PATH ":" ${stdenv.lib.makeBinPath [
	"$out" which libcdio-paranoia cddiscid wget
	vorbis-tools id3v2 eyeD3 lame flac glyr
	]}

	makeWrapper ${jre}/bin/java $out/bin/astah \
	--add-flags "-jar $out/share/astah/astah-community.jar"

marvin: init at 19.1.0 #53839

marvin: init at 19.1.0 #53839

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fusion809 commented Jan 12, 2019 • edited Loading

Motivation for this change

Things done

Area that could do with some improvement

fusion809 commented Jan 12, 2019 • edited Loading

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