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Old 04-27-2013, 04:35 PM   #1
anzdro
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Default Installing bowtie2 to computer

Hello,

I tried usiing tophat and got a message that I need to use a bowtie2 alignment instead of bowtie, so, I downloaded the zip package for bowtie2. I was able to get bowtie2-build installed on my computer, but I am unable to get 'bowtie2' working. Whenever I try to it gives me the following message:

Error: Expected bowtie2 to be in same directory with bowtie2-align...

I'm not sure what to do from here. Any help is greatly appreciated!

Best,
Anzdro
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Old 04-28-2013, 06:03 AM   #2
GenoMax
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Default

You have presumably done the first step "Building from source" here. But have you done the second "Adding to PATH".
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Old 04-28-2013, 10:09 AM   #3
anzdro
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I have tried to install from source and got the following message:
/usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 \"" \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \
\
-o bowtie2-build bt2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \
-lpthread
/bin/sh: 1: /usr/bin/g++: not found
make: *** [bowtie2-build] Error 127
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Old 04-28-2013, 11:46 AM   #4
GenoMax
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What OS are you using? Looks like you are missing a compiler.

Note: You do not have to compile bowtie locally (if you had downloaded the pre-compiled version) but depending on where you installed the downloaded binary you will want to append the path using the second link in my first post.
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Old 04-28-2013, 12:21 PM   #5
anzdro
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I'm using Ubuntu 64 bit.
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Old 04-28-2013, 01:52 PM   #6
GenoMax
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Do you want to compile the software yourself or use the pre-compiled binary? Depending on we can give you additional directions.

In either case you will have to append your PATH variable so bowtie2 can be found by Tophat. Here are directions on how to do this on Ubuntu.
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Old 08-02-2013, 04:03 PM   #7
C9r1y
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Default Error: Expected bowtie2 to be in same directory with bowtie2-align

I am having the same problem, but trying to install Bowtie2 to a linux server. I get the same error when just trying to run Bowtie2 to test the installation:

Error: Expected bowtie2 to be in same directory with bowtie2-align

Any insights? I appreciate it.
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Old 01-03-2014, 06:05 AM   #8
chrisbala
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Default me too

same problem here... bowtie2 runs fine if I am running tophat, but if I try to run bowtie2 directly, I am having the same issue.
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Old 01-03-2014, 06:09 AM   #9
dpryan
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Just put bowtie2-align in the same directory as bowtie2 then (bowtie2 is just a perl program that runs bowtie2-align).
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Old 01-03-2014, 06:09 AM   #10
GenoMax
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Quote:
Originally Posted by chrisbala View Post
same problem here... bowtie2 runs fine if I am running tophat, but if I try to run bowtie2 directly, I am having the same issue.
Do you know where your bowtie2 programs are located?

Code:
$ which bowtie2

$ which bowtie2-align
Are those two in the same directory?
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Old 01-03-2014, 06:20 AM   #11
chrisbala
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Default thanks!

Got it...

had bowtie2 in two places

/usr/local/bin

and

/usr/local/bin/bowtie2.2blahblah/

bowtie2-build was only in the latter.

Not sure how that happened, but must have done something dumb..
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