Tophat ./configure error

[repinementer]

Hi guys
I'm trying to install tophat using cygwin on windows
when I ran ./configure command I got the following error
Could you please suggest me anything that can solve this error

Thanx

$ ./configure --prefix=/cygdrive/c/Documents\ and\ Settings/bogugk/Desktop/tophat-1.0.13/

./configure: line 14: $'\r': command not found
./configure: line 25: syntax error near unexpected token `$'in\r''
'/configure: line 25: `  case `(set -o) 2>/dev/null` in

FYI: For me it seems newline problem '\r' instead of '\n', but I have no idea what and where to change

I deleted one extraline at 14 and the errors reduced to 2

./configure: line 25: syntax error near unexpected token `$'in\r''
'/configure: line 25: `  case `(set -o) 2>/dev/null` in

[raela]

The problem is Linux (and I think Unix in general) uses only \n as a newline character. whereas Windows uses \n\r for newlines. I don't know all of the commands cygwin comes with, but I would try:
sed -e 's/\r$//' configure > config.new # DOS to UNIX (removing CRs)
egrep -L $'\r\n' configure > config.new # show UNIX style file (LF terminated)
grep -PL $'\r\n' configure > config.new # show UNIX style file (LF terminated)
From there, you should be able to do ./config.new, or rename configure to something else and rename config.new to configure.

[repinementer]

thanx for the suggestions

it gave the following error.

$ ./configure --prefix=/cygdrive/c/Documents\ and\ Settings/bogugk/Desktop/tophat-1.0.13/

configure: error: cannot run /bin/sh config/config.sub

[raela]

I did a quick google search, but I just want to make sure - did you install the development tools? (gcc, make, etc). Also, remove the tophat dir and this time unpack it using cygwin, not windows. Try `tar zxvf tophat-1.0.13.tar.gz` in cygwin.

[repinementer]

heyyyyyy

Yes I already installed all tools.
untar command worked liked charm.
I installed after using untar from cygwin. WOW

but after runnig make I got the following error.
Is tophat BETA version only works with 64 bit computers?

make
make all-recursive
make[1]: Entering directory `/cygdrive/c/Documents and Settings/bogugk/Desktop/tophat-1.0.13'
Making all in src
make[2]: Entering directory `/cygdrive/c/Documents and Settings/bogugk/Desktop/tophat-1.0.13/src'
g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -m64 -O3 -DNDEBUG -I./SeqAn-1.1 -Wall -g -m64 -O3 -DNDEBUG -MT reads.o -MD -MP -MF .deps/reads.Tpo -c -o reads.o reads.cpp
reads.cpp:1: sorry, unimplemented: 64-bit mode not compiled in
In file included from /usr/lib/gcc/i686-pc-cygwin/4.3.4/include/c++/bits/stl_algobase.h:66,
from /usr/lib/gcc/i686-pc-cygwin/4.3.4/include/c++/bits/char_traits.h:46,
from /usr/lib/gcc/i686-pc-cygwin/4.3.4/include/c++/string:47,
from reads.cpp:15:
.......................
..........................
make[1]: *** [reads.o] Error 1
make[1]: Leaving directory `/cygdrive/c/Documents and Settings/bogugk/Desktop/tophat-1.0.13/src'
make: *** [install-recursive] Error 1

[repinementer]

is it space problem. My machine only has 3GB ram and 160 HD

is it space problem. My machine only has 3GB ram and 160 HD

[john_mu]

hmm 3Gb RAM is a bit low to run TopHat. On some settings I have seen it use upwards of 12GB...

Also, the current way it implements sorting the SAM file will easily use over 5GB.

That is, you will need 5GB of free RAM or about 8GB total.

EDIT: Actually, that depends on how many reads you have and which genome. Which genome are you interested in?

[repinementer]

Thanx

Ya you are right. Thanx
I just came to know that.
Human genome so it will be really huge.