Issues making Jvarkit

[X-24]

Here it s, i REALLY REALLY need to use Biostar 94573 to convert some FASTA files into VCF so i will try again cause i have no other choices (even top Bioinformatics software like Artemis or Geneious cannot accept FASTA as an input and produce VCF as an output). I succesfully installed make, and successfully "made" curl.

When i run the first command line of your example:

$ curl https://raw.githubusercontent.com/biopython/biopython/master/Tests/Clustalw/opuntia.aln

(Actually in the example you provide in "https://github.com/lindenb/jvarkit/wiki/Biostar94573" the adress is https://raw.github.com/biopython/biopython/master/Tests/Clustalw/opuntia.aln and i had to change it to https://raw.githubusercontent.com/biopython/biopython/master/Tests/Clustalw/opuntia.aln but that's just a detail !)

I get the same output as you : CLUSTAL W (1.81) multiple sequence alignment

gi|6273285|gb|AF191659.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273284|gb|AF191658.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273287|gb|AF191661.1|AF191 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273286|gb|AF191660.1|AF191 TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273290|gb|AF191664.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273289|gb|AF191663.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA gi|6273291|gb|AF191665.1|AF191 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA *** ** ***

gi|6273285|gb|AF191659.1|AF191 TATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATA gi|6273284|gb|AF191658.1|AF191 TATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATA gi|6273287|gb|AF191661.1|AF191 TATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATA gi|6273286|gb|AF191660.1|AF191 TATATA----------ATATATTTATAATTTCCTTATATATCCAAATATA gi|6273290|gb|AF191664.1|AF191 TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA gi|6273289|gb|AF191663.1|AF191 TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA gi|6273291|gb|AF191665.1|AF191 TATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATA \ ** ** * *****

gi|6273285|gb|AF191659.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGT gi|6273284|gb|AF191658.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273287|gb|AF191661.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273286|gb|AF191660.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273290|gb|AF191664.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT gi|6273289|gb|AF191663.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTAT gi|6273291|gb|AF191665.1|AF191 AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT ****** * *

gi|6273285|gb|AF191659.1|AF191 ACCAGA gi|6273284|gb|AF191658.1|AF191 ACCAGA gi|6273287|gb|AF191661.1|AF191 ACCAGA gi|6273286|gb|AF191660.1|AF191 ACCAGA gi|6273290|gb|AF191664.1|AF191 ACCAGA gi|6273289|gb|AF191663.1|AF191 ACCAGA gi|6273291|gb|AF191665.1|AF191 ACCAGA

---

But when i try to make any tool, i still got an error message saying :

makefile:167: multiple target patterns. Stop.

I made sure i had Java 1.7, when i run "java -version" i get :

Java version "1.7.0_51" Java(TM) SE Runtime Environment (build 1.7.0_51-b13) Java HotSpot(TM) Client VM (build 24.51-b03, mixed mode, sharing)

I also added every single possible required folder to my PATH to make sure i had all the requisite folders in it. Here is my PATH :

C:\ProgramFiles\OpenVPN\bin;C:\;C:\mingw\msys\1.0\bin;C:\mingw\msys\1.0\lib;C:\mingw\bin;C:\mingw\lib;C:\Perl\bin;C:\Perl\lib;C:\Perl;C:\mingw\msys;C:\mingw;C:\curl-7.43.0;C:\Program Files\Git\bin;C:\Program Files\Git\lib;C:\Program Files\Git;C:\Program Files\Java\jdk.1.7.0_79;C:\Program Files\Java\jdk.1.7.0_79\bin;C:\Program Files\Java\jdk.1.7.0_79\Git\bin;C:\Program Files\Java\jdk.1.7.0_79\Git;C:\Program Files\Java\jdk.1.7.0_79\apache-ant-1.9.5;C:\Program Files\Java\jdk.1.7.0_79\Git;C:\Program Files\Java\jdk.1.7.0_79/bin;C:\Program Files\Java\jdk.1.7.0_79\Git;C:\Program Files\Java\jre7;C:\Program Files\Java\jre7/bin;C:\Program Files\Java\jre7/lib;

and finally, googling my error i was told by two different websites to check for colons in target names so i copied and pasted the makefile in word and searched for colons but word did not found a single one. I re downloaded jvarkit using the git clone command :

$ git clone "https://github.com/lindenb/jvarkit.git"

a few days ago so i guess i have the latest version of javrkit.

Please, could you try to help me ?

[lindenb]

• what's your OS
• what's your version of GNU make ?

[X-24]

OS is Windows 7 Edition Starter GNU Make is version 3.81

[lindenb]

what do you mean with

But when i try to make any tool

[X-24]

when i either try to run just

$ make

from the jvarkit directory, or when y try

$ make biostar94573

or any other tool instead of biostar94573 (like the vcffilterjs of your example)

[lindenb]

$ make

should print:

This is the top target. Run 'make name-of-target' to build the desired target. Run 'make all' if you're Pierre Lindenbaum

also, you should have:

$ shasum Makefile 
716b85b0bb39557e49cfb752bb15aca07ddf080e  Makefile

[lindenb]

ah, I think I've got it: http://stackoverflow.com/questions/14514086/make-multiple-target-patterns-stop

because you're using windows, Make inserts some ':' in the file full paths, and a colon is a reserved word for GNU make, it breaks everything.

I'm sorry, I won't fix this.

[X-24]

Euh Okay, people who successfuly run it are on Linux i guess, do you think it might work on Mac Os ?

[lindenb]

MacOs / Linux: yes