Bowtie2 and Bowtie2-align error

Question

[Azhar]

Hi i know its just a kind of basic question but unfortunallty i have some problem with this issue,

I am using remote server, so after installing bowtie2 i run from my account as

$bowtie2

it gives out put error like

(ERR): Expected bowtie2 to be in same directory with bowtie2-align:
/home/SXY8/azhar/bowtie2-2.3.2-legacy/

but when i find the path for

$which bowtie2

it gives

(ERR): Expected bowtie2 to be in same directory with bowtie2-align:
/home/SXY8/azhar/bowtie2-2.3.2-legacy/

but when i run

$which bowtie2-align

it gives error like

/usr/bin/which: no bowtie2-align in (/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/SXY8/azhar//bin:/home/SXY8/azhar//twoBitToFa://home/SXY8/azhar//bin:/home/SXY8/azhar//bowtie2-2.3.2-legacy://home/SXY8/azhar//bin:/home/SXY8/azhar//bowtie2-align://home/SXY8/azhar//bin:/home/SXY8/azhar//bowtie2-align://home/SXY8/azhar//bin:/home/SXY8/azhar//bowtie2-2.3.2-legacy://home/SXY8/azhar//bin:/home/SXY8/azhar//bowtie2-2.3.2-legacy/botwie2-align://home/SXY8/azhar//bin:/home/SXY8/azhar//bowtie2-2.3.2-legacy/://home/SXY8/azhar//bin:/home/SXY8/azhar//bowtie2-2.3.2-legacy/://home/SXY8/azhar//bin:/home/SXY8/azhar//bowtie2-2.3.2-legacy/:/home/SXY8/azhar//bin:/home/SXY8/azhar//botwie2-align:/home/SXY8/azhar//bin:/home/SXY8/azhar//botwie2)

I tried to give them same path but still have issue. I read some related problems from internet they say that may have the issue with g++ but I have so sudo authority to install g++ or update, but still I am not clear about the problem.

[Medhat]

why you do not use the binary version ?

[Devon Ryan]

How did you install bowtie2?

[Azhar]

I download bowtie2 from source forge as link is given in manual of Bowtie2 ,download unpack means unzip place in my login folder and then add the path , I check the path its added in oath but still can run it and error is same

PATH=/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/SXY8/azhar//bin:/home/SXY8/azhar//twoBitToFa:/home/SXY8/azhar//bin:/home/SXY8/azhar//bowtie2-2.3.2-legacy://home/SXY8/azhar//bin:/home/SXY8/azhar//bowtie2-2.3.2 as we can see its present in path but stii has the same erroe when i try to check or run it like $bowtie2 PATH=/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/SXY8/azhar//bin:/home/SXY8/azhar//twoBitToFa:/home/SXY8/azhar//bin:/home/SXY8/azhar//bowtie2-2.3.2-legacy://home/SXY8/azhar//bin:/home/SXY8/azhar//bowtie2-2.3.2

[Medhat]

sorry but after unzip the folder did you use make ?

[Azhar]

No because there is no make file but i still tried it did not work Becuase there is no make file

[Pierre Lindenbaum]

No because there is no make file but i still tried it did not work Becuase there is no make file

this is wrong. I've just downloaded https://netcologne.dl.sourceforge.net/project/bowtie-bio/bowtie2/2.3.2/bowtie2-2.3.2-source.zip

there IS a Makefile

[Azhar]

yes you are right source code have make file but i used the complied version, but i also used source version and cd into bowtie and make and it give error like

for all of its sub files gives similer error like this

bowtie_build_main.cpp:25: threading.h:29:24: fatal error: tbb/mutex.h: No such file or directory # include <tbb mutex.h=""> ^ compilation terminated. make: * [bowtie2-build-s] Error 1

[Devon Ryan]

If you downloaded the binary, then you should have ended up with both bowtie2-align and bowtie2. Just redownload, unpack, and copy everything to your PATH.

[Azhar]

I download bowtie2-2.3.2-source now and try using make , but still it gives this error last few lines like this compilation terminated. In file included from ds.h:30:0, from bowtie_build_main.cpp:25: threading.h:29:24: fatal error: tbb/mutex.h: No such file or directory # include <tbb mutex.h=""> ^ compilation terminated. make: * [bowtie2-build-s] Error 1

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

[hz_ghosta]

Hi, I am also puzzled in this problem. Ubuntu showed " Expected bowtie2 to be in same directory with bowtie2-align:/usr/local/bin/bowtie2-2.4.4-source/bowtie2-2.4.4/". So have you solve the problem? Although 4 years have passed.