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Old 04-10-2015, 11:56 AM   #1
nimrod337
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Default Expected bowtie2 to be in same directory with bowtie2-align

Okay, sorry if this is a little newbish, but I cannot seem to get bowtie2 to run on my mac OS terminal for the life of me. When I run the 'bowtie2' command I get the error "Expected bowtie2 to be in same directory with bowtie2-align"

I can see that this is in fact true. In the unzipped bowtie2 folder I see bowtie2*, bowtie2-build*, and bowtie2-inspect*

I saw someone had this problem in a different thread and the person resolved the issue by finding the correct paths to bowtie2 and bowtie2-align by using the

$which bowtie2
$which bowtie2-align

However, this is where I am stuck. when I run the "which command in the terminal, it just brings up a new $ line. It doesn't print any path... This is the same for samtools (which I have been able to run successfully already). This problem is essentially impossible to google, because the word "which" is almost exclusively ignored by the search engine.
the $which command works perfectly fine for normal executables such as mkdir, touch, et cetera...

On a related note, I have installed blast+ so I can make blast databases, and perform blast searches locally, and it installs to the usr/bin/ncbi without me even moving it, or anything. This differs greatly from the other programs that I just download the zipped file from sourceforge, unzip, and make in terminal.

I know the second step in a lot of these bioinformatic programs is to add them to the $PATH, but I've never been too clear on what that is, or how it's done (I've honestly tried to do some reading on that issue, and all of it is either super vague, or just skips past the part I am not clear on.) If anyone has some literature or links that can explain this portion of UNIX command line as if I was 5 years old, I would be forever grateful.
There seems to be a large gap in the available information from what UNIX command line is, and how to actually download source files, and compile them in a way that is helpful, and somewhat futureproof. If anyone knows of a good book, or wiki that sort of starts from the ABSOLUTE bottom, and goes all the way up to fancy bioinformatics, I would be forever grateful.

Thanks so much, this forum is a real lifesaver sometimes!
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Old 04-10-2015, 02:39 PM   #2
GenoMax
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Once you download the precompiled binary zip file OS X should have uncompressed it once you double clicked on the file.

At this point you can move the "bowtie2-2.2.5" directory to a location you want (optional). Then you should be able to run bowtie2 by providing

Code:
$ /path_to/bowtie2-2.2.5/bowtie2
If you are inside the bowtie2-2.2.5 directory then doing the following should work.

Code:
$ ./bowtie2 -h
There is a great basic unix tutorial for biologists at Korf lab site: http://korflab.ucdavis.edu/Unix_and_...ent.html#part1

BTW: Did you get the OS X binary from this link: http://sourceforge.net/projects/bowt...owtie2/2.2.5/?
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Old 04-11-2015, 01:09 PM   #3
nimrod337
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Thanks for your reply! That is exactly where I downloaded the source file from. I have unzipped and moved it into my "bioinformatics/programs" folder. I am currently in the directory where the bowtie2 executable is, and that is when I get that error. I don't know if it's specific to bowtie2 because I was able to run bowtie and BWA and Samtools without incident... I still don't like that I can't see the path by using "$which"...
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Old 04-11-2015, 01:38 PM   #4
GenoMax
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If you are in the directory where the bowtie2 executables are then the second command above should work. Does this not print help text to screen?

Code:
$ ./bowtie2 -h
Apple does things differently (I have not found how to force the database update for "which" as yet) compared to "which" on linux.

If you want to find files you can use mdfind command (which should generate which equivalent output).

Code:
$ mdfind "kMDItemDisplayName == bowtie2"

$ mdfind -name bowtie2
Second option will generate a list of all objects that have bowtie2 somewhere.

It is possible that you have bowtie2 in some other path on the system that is being executed preferentially than the one in the directory you are in.

Last edited by GenoMax; 04-11-2015 at 01:42 PM.
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Old 04-11-2015, 01:54 PM   #5
GenoMax
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You could also try this: https://coderwall.com/p/eexczq/updat...-back-updatedb and then use the locate command as an option.

At least for me, locate does not find bowtie2 after the database upgrade (OS X yosemite). YMMV.
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