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Old 06-14-2012, 02:26 AM   #1
pepsimax
Junior Member
 
Location: London

Join Date: May 2012
Posts: 9
Default Installing SplitRead

Hi,

I'm fairly new to this sort of work, and I've been having trouble installing SplitRead (http://splitread.sourceforge.net/manual.html). It requires MrsFast and Samtools, both of which I've installed and got working properly. I'm running Fedora 16, I downloaded the tar.gz, decompressed it and got Code-Release. That contains
breakReads.c Make.sh split_match_sam.c
fastqdeloea.c Paired-end_match_sam.c SplitOEA_match.c
Finalevents_v5.c pair_match_v5.c SplitReadAll_lite.c
getFinalevents.sh pairToSC.sh

I tried
Code:
Bash Make.sh
and
Code:
sh Make.sh
after making it executable with
Code:
chmod -x
. All I get in return is a string of errors.

Code:
bash-4.2$ bash Make.sh
mkdir: cannot create directory `/___': File exists
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
Paired-end_match_sam.c: In function ‘myfopen’:
Paired-end_match_sam.c:242:9: warning: assignment from incompatible pointer type [enabled by default]
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
pair_match_v5.c: In function ‘myfopen’:
pair_match_v5.c:516:9: warning: assignment from incompatible pointer type [enabled by default]
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
split_match_sam.c: In function ‘myfopen’:
split_match_sam.c:227:9: warning: assignment from incompatible pointer type [enabled by default]
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
SplitOEA_match.c: In function ‘myfopen’:
SplitOEA_match.c:245:9: warning: assignment from incompatible pointer type [enabled by default]
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
cp: cannot stat `breakReads': No such file or directory
cp: cannot stat `fastqdeloea': No such file or directory
cp: cannot stat `events5': No such file or directory
cp: cannot stat `Paired-end_match_sam': No such file or directory
cp: cannot stat `pair_match_v5': No such file or directory
cp: cannot stat `split_match_sam': No such file or directory
cp: cannot stat `SplitOEA_match': No such file or directory
cp: cannot stat `SplitReadAll_lite': No such file or directory
I guess I'm missing something simple... please help!
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