[GenoMax]

Joana Teixeira@Joana /c/bedtools
$ curl http://bedtools.googlecode.com/files....2.23.0.tar.gz > BEDTools.t
ar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 1453 100 1453 0 0 4429 0 --:--:-- --:--:-- --:--:-- 4429

Joana Teixeira@Joana /c/bedtools
$ tar -zxvf BEDTools.tar.gz

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now

See if you can use gunzip to extract followed by tar.

[JoanaTeixeira]

Joana Teixeira@Joana /c/bedtools
$ curl http://bedtools.googlecode.com/files....2.23.0.tar.gz > BEDTools.t
ar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 1453 100 1453 0 0 4429 0 --:--:-- --:--:-- --:--:-- 4429

Joana Teixeira@Joana /c/bedtools
$ tar -zxvf BEDTools.tar.gz

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now

[JoanaTeixeira]

I tried to do this, but it didn't work.

I followed these steps:

(http://bedtools.readthedocs.org/en/l...llation.html)- Compiling from source via Google Code.

[GenoMax]

I think you have compiled other software yourself so why not do "bedtools" the same way. Get the source code and compile it. Do not worry about brew.

[JoanaTeixeira]

I searched for brew on my computer and I don't found.
I think that installation is failing and I don’t know why.

[GenoMax]

$ brew install bedtools
sh: brew: command not found

Try (if brew file is in current directory then omit the /path_to/ part).

$ /path_to/brew install bedtools

If that does not work then

$ chmod u+x /path_to/brew
$ /path_to/brew install bedtools

[JoanaTeixeira]

Yes, you are right.
I fixed my mistake but something isn´t OK:

Joana Teixeira@Joana /c/curl/samples
$ ruby -e "$(curl -k https://raw.githubusercontent.com/Ho...nstall/master/
install)"
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 7859 100 7859 0 0 9678 0 --:--:-- --:--:-- --:--:-- 9678

Joana Teixeira@Joana /c/curl/samples
$ brew install bedtools
sh: brew: command not found

[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").

[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]

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]

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]

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]

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]

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]

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