I think you're facing two different problems here.
For the samtools I see you're doing this on windows so you should probably run
make on the 'Makefile.mingw' file instead e.g.
$ make -f Makefile.mingw
For bcftools it is simply due to the space in the path 'make'. By default linux
programs use spaces to separate executables from their arguments. Whereas
Windows often has spaces in places where linux wouldn't expect them. The
command is failing because it thinks 'C:/Program' is the executable and
'Files/GnuWin32/bin/make lib-static' are the parameters. Not 'C:/Program
Files/GnuWin32/bin/make' and 'lib-static'. I'm not quite sure how you'd fix
this, though.
Chris
From: Xavier Olessa-Dragon <xavi...@hotmail.fr<mailto:xavi...@hotmail.fr>>
Date: Saturday, 14 November 2015 17:00
To: samtools
<samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>>
Subject: [Samtools-help] I can't make Samtools from the Makefile
Hi,
first of all i am an absolute novice, i never used neither make or git before
and only installed them and familiarized with them in order to use samtools,
bcftools and other bio informatics tools (i am Biology Student and i am
particulary interested by the tools that allow to move between FASTA and VCF
files). When i cd to either the samtools folder or the bcftools folder and try
to "make" them as instructed, i receive error messages that i added. I
absolutely do not rule out that i dot installed make right or did not set a
correct PATH. Those are the error messages (the quote signs are added and are
not part of what is on screen".
"Acer@PC-de-Acer MINGW32 ~/samtools-1.2
$ make
gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
-I. -Ihtslib-1.2.1 -c -o bam_index.o bam_index.c
process_begin: CreateProcess(NULL, gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64
-D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -Ihtslib-1.2.1 -c -o bam_index.o
bam_index.c, ...) failed.
make (e=2): Le fichier sp▒cifi▒ est introuvable.
make: *** [bam_index.o] Erreur 2 "
"
Acer@PC-de-Acer MINGW32 ~/bcftools-1.2
$ make
cd htslib-1.2.1 && C:/Program Files/GnuWin32/bin/make lib-static
/usr/bin/sh: C:/Program: No such file or directory
make: *** [htslib-1.2.1/libhts.a] Erreur 127 "
Could you help me please ?
Thanks a lot
Best Regards
Sylene Mythridate
The University of Dundee is a registered Scottish Charity, No: SC015096
------------------------------------------------------------------------------
Presto, an open source distributed SQL query engine for big data, initially
developed by Facebook, enables you to easily query your data on Hadoop in a
more interactive manner. Teradata is also now providing full enterprise
support for Presto. Download a free open source copy now.
http://pubads.g.doubleclick.net/gampad/clk?id=250295911&iu=/4140
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
