bowtie 2 on windows 8

[JoanaTeixeira]

Hello,
I have tried install bowtie 2 on windows 8, but I failed.

Someone help me, please?

[Ahaswer]

Hi Joana,
can you describe your failure? Have you downloaded correct release?

[JoanaTeixeira]

Thanks for helping me.
I will explain the main steps that I did:
1. Download bowtie2-2.2.5-source.zip (http://sourceforge.net/projects/bowt...bowtie2/2.2.5/)
2. Unzip the document to my desktop
3. Download and install TDM Compiler Package (http://tdm-gcc.tdragon.net/)
4. Open MingGW Command prompt
5. Write: cd C:\Users\Joana Teixeira\Desktop\bowtie2-2.2.5-source\
an error appear:” sh: cd: UsersJoana: No such file or directory”.

I tried many things to fix this error (change the place of the file…. Edit the makefile…mingw..cypwin..), but nothing result.
I don't have many experience with this type of programs (I am starting now). And I can't find a website or a tutorial that can help me in my first steps.

[jwfoley]

Have you used the command prompt before? It looks like you're having trouble just changing to a new directory, before you even start working with Bowtie. (Specifically because you have a space in the path; put quotation marks around it.) You may want to look at alternative ways of using Bowtie, like Galaxy or Basespace.

[JoanaTeixeira]

No, I haven't.
I found that I forgot to install a important package.
Now, I am having a new problem.
I can change the directory, but then I do "make", some errors appear, like: diff_sample.h:573......

[GenoMax]

@Joana: Please post complete error output. We can't see your screen/computer so posting only snippets of errors doesn't help us.

[jwfoley]

It looks like you are struggling with the basics of the CLI, and this question is not specific to Bowtie in particular or to bioinformatics in general. You may be able to get better help from a general MingGW or Linux/Unix CLI support forum (not sure if the Unix/Linux Stack Exchange can help with MingGW), or an introductory class. I'll reiterate that there are alternatives to using the CLI in the first place, as that's a lot of skills to learn just to run one program.

[JoanaTeixeira]

this is what I get.
Sorry, I can't copy the full errors that appears.

[GenoMax]

Can you scroll up (to about the point where you think the first "error" shows up) and then post that screen shot?

It may be better to copy and paste text from the terminal (rather than screenshot). This is how you can do that. Even though the link refers to XP this should work for all windows versions: https://www.microsoft.com/resources/....mspx?mfr=true

[JoanaTeixeira]

Thanks for helping me.
Finally I put the bowtie2 running.
But when I tried running bowtie2-build, bowtie2-inspect, an error appear:

"/usr/bin/env: python: No such file or
directory"

[GenoMax]

Looks like you need to install python (http://www.anthonydebarros.com/2014/...n-windows-8-1/). Install python v.2.7 first to see if that works.

[JoanaTeixeira]

Thank you for your help. It works now.
I have a new problem with SAMtools.
I did the download here: http://sourceforge.net/projects/samt...s/samtools/1.2)
I unzipped the file and I wrote:

cd C:/samtools-1.2/
makefile.mingw

And some errous appear:

Joana Teixeira@Joana ~
$ cd C:/samtools-1.2/

Joana Teixeira@Joana /c/samtools-1.2
$ makefile.mingw
gcc.exe: no input files
Usage: ar.exe [emulation options] [-]{dmpqrstx}[abcfilNoPsSuvV] [member-name] [c
ount] archive-file file...
ar.exe -M [<mri-script]
commands:
d - delete file(s) from the archive
m[ab] - move file(s) in the archive
p - print file(s) found in the archive
q[f] - quick append file(s) to the archive
r[ab][f][u] - replace existing or insert new file(s) into the archive
t - display contents of archive
x[o] - extract file(s) from the archive
command specific modifiers:
[a] - put file(s) after [member-name]
[b] - put file(s) before [member-name] (same as [i])
[D] - use zero for timestamps and uids/gids
[N] - use instance [count] of name
[f] - truncate inserted file names
[P] - use full path names when matching
[o] - preserve original dates
[u] - only replace files that are newer than current archive contents

generic modifiers:
[c] - do not warn if the library had to be created
[s] - create an archive index (cf. ranlib)
[S] - do not build a symbol table
[T] - make a thin archive
[v] - be verbose
[V] - display the version number
@<file> - read options from <file>
emulation options:
No emulation specific options
ar.exe: supported targets: pe-i386 pei-i386 elf32-i386 elf32-little elf32-big sr
ec symbolsrec verilog tekhex binary ihex
./makefile.mingw: line 3: -g: command not found
./makefile.mingw: line 4: -D_USE_KNETFILE: command not found
./makefile.mingw: line 5: knetfile.o: command not found
./makefile.mingw: line 6: KNETFILE_O: command not found
./makefile.mingw: line 6: bgzf.o: command not found
./makefile.mingw: line 9: bam_tview.o: command not found
./makefile.mingw: line 13: bcftools/bcf.o: No such file or directory
./makefile.mingw: line 16: samtools.exe: command not found
./makefile.mingw: line 17: -I.: command not found
./makefile.mingw: line 18: .: filename argument required
.: usage: . filename [arguments]

I know that something is wrong because I wrote:

samtools view -bS eg2.sam > eg2.bam
sh: samtools: command not found.

I don't know that I am doing wrong and I didn't a good website that help me to install the samtools.

Help me, please?
Thank you!

[GenoMax]

TopHat/Bowtie may not work with new version (v. 1.x) of samtools. You should try installing older version (v. 0.1.19).

Quote from TopHat site

TopHat 2.0.13 release 10/2/2014
Version 2.0.13 is a maintenance release with the following changes:

removed SAMtools as an external dependency in order to avoid incompatibility issues with recent and future changes of SAMtools and its code library (an older, stable SAMtools version is now packaged with TopHat)

[JoanaTeixeira]

Thanks.
Samtools is running.
Now, I need to install bedtools (http://bedtools.readthedocs.org/en/l...tallation.html).
First, I'm trying to install homebrew (http://brew.sh/)
When I wrote

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

an error appears:
sh: ruby: command not found
sh: curl: command not found

So, I tried to install curl (http://curl.haxx.se/download.html) and ruby (http://rubyinstaller.org/).

I tried again:
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

And a error appears again:
$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com7Homebrew/install/mast
er/install)"
curl: (6) Could not resolve host: raw.githubusercontent.com7Homebrew


Same help or suggestion?

I also need to install bedtools.

Thanks

[GenoMax]

And a error appears again:
$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com7Homebrew/install/mast
er/install)"
curl: (6) Could not resolve host: raw.githubusercontent.com7Homebrew

Thanks

Looks like mistyped "/" between the com and homebrew (instead typed a "7").