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Old 11-27-2012, 05:02 AM   #1
jorhodes
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Location: UK

Join Date: Nov 2012
Posts: 7
Default SAMtools will not compile - help please!

Hi all,

I am having trouble compiling SAMtools i.e. when I type 'make' in the Unix Terminal, I get the following error:

make[2]: Nothing to be done for `lib'.
/bin/sh: line 0: cd: /Users/Jo: No such file or directory
make[2]: Nothing to be done for `lib'.
/bin/sh: line 0: cd: /Users/Jo: No such file or directory
/bin/sh: line 0: cd: misc: No such file or directory
make[2]: Nothing to be done for `lib'.
/bin/sh: line 0: cd: /Users/Jo: No such file or directory
make[1]: *** [lib-recur] Error 1
make: *** [all-recur] Error 1

I assume there's a library missing. I have zlib, and have compiled razip.

This is samtools-0.1.18 on a Mac OS X Lion (10.8.2).

Any help would be appreciated!

Jo
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Old 11-27-2012, 05:44 AM   #2
jiaco
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This line right here: "cd: /Users/Jo: No such file or directory"
is giving you a hint? Does the path exist? Maybe your username has a space in it?
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Old 11-27-2012, 05:59 AM   #3
jorhodes
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Yes there is a space - but I'm not really sure how I can get the 'make' command to overcome this?
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Old 11-27-2012, 06:34 AM   #4
jiaco
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make a new user without any spaces and build it under that user.
otherwise you will have to edit the makefiles and put quotes around the path...
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Old 11-27-2012, 07:40 AM   #5
jorhodes
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Making a new user seemed excessive so I just put quotations around the paths in the 'makefile' - sorted! Thanks
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