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 ?