Issue with bowtie (Rikesh)

[Dilawar Singh]

Creating a new thread.

Hi Dilawar,
    I am trying to install Bowtie (binary downloaded from http://sourceforge.net/projects/bowtie-bio/files/bowtie/) on nargis server.
There is Makefile in downloaded directory and so when I typed make, it started writing-

       ~ /usr/bin/g++ -O3 -m64 -msse2  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2  -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
        -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 \
         -I third_party \
        -o bowtie2-build-s 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
/usr/bin/g++ -O3 -m64 -msse2  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2  -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
        -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 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
         -I third_party \
        -o bowtie2-build-l 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 ~

After writing 3-4 times the same above thing it got stopped saying -
$ Write failed: Broken pipe

when I again typed make it says-
make: Nothing to be done for `all'

I could see some additional file generated in the downloaded directory, due to previous process.

[Dilawar Singh]

Here is what I did to install BowTie on Nargis. This is easier to install.

0. My user path is `~/bin`, in your case, it could be different.
1. Downloading bowtie using wget, and unzip it. (Mind the architecture, Since cluster is 64bit, I am download x86_64.zip file, otherwise it would be either i686 or i383).

$ wget http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-linux-x86_64.zip
--2015-05-12 09:58:46--  http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-linux-x86_64.zip
Resolving proxy.ncbs.res.in... 192.168.0.4
Connecting to proxy.ncbs.res.in|192.168.0.4|:3128... connected.
Proxy request sent, awaiting response... 302 Moved Temporarily
Location: http://softlayer-sng.dl.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-linux-x86_64.zip [following]
--2015-05-12 09:58:47--  http://softlayer-sng.dl.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-linux-x86_64.zip
Connecting to proxy.ncbs.res.in|192.168.0.4|:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 26413746 (25M) [application/octet-stream]
Saving to: "bowtie2-2.2.5-linux-x86_64.zip"

100%[=============>] 26,413,746  46.1M/s   in 0.5s    

2015-05-12 09:58:48 (46.1 MB/s) - "bowtie2-2.2.5-linux-x86_64.zip" saved [26413746/26413746]

Unzipping it to one of your path e.g. $HOME/bin

$ unzip bowtie2-2.2.5-linux-x86_64.zip -d ~/bin
Archive:  bowtie2-2.2.5-linux-x86_64.zip
   creating: /home/dilawar/bin/bowtie2-2.2.5/
  inflating: /home/dilawar/bin/bowtie2-2.2.5/AUTHORS
  inflating: /home/dilawar/bin/bowtie2-2.2.5/bowtie2
  inflating: /home/dilawar/bin/bowtie2-2.2.5/bowtie2-align-l
  inflating: /home/dilawar/bin/bowtie2-2.2.5/bowtie2-align-l-debug
  inflating: /home/dilawar/bin/bowtie2-2.2.5/bowtie2-align-s
  inflating: /home/dilawar/bin/bowtie2-2.2.5/bowtie2-align-s-debug
  inflating: /home/dilawar/bin/bowtie2-2.2.5/bowtie2-build
  inflating: /home/dilawar/bin/bowtie2-2.2.5/bowtie2-build-l
  inflating: /home/dilawar/bin/bowtie2-2.2.5/bowtie2-build-l-debug
  inflating: /home/dilawar/bin/bowtie2-2.2.5/bowtie2-build-s
  inflating: /home/dilawar/bin/bowtie2-2.2.5/bowtie2-build-s-debug
  inflating: /home/dilawar/bin/bowtie2-2.2.5/bowtie2-inspect
  inflating: /home/dilawar/bin/bowtie2-2.2.5/bowtie2-inspect-l
  inflating: /home
.....



4. Next just check that `~/bin/bowtie2-2.2.5` is in your $PATH. If not, in ~/.bashrc file add the following line, (mind the spelling, open the file in gedit).

           $ gedit ~/.bashrc

Add the following line,
export PATH=$HOME/bin/bowtie2.-2.2.5:$PATH

Then source the .bashrc file to update the path.

$ source ~/.bashrc

$ echo $PATH

$ which bowtie2

Last command should give you a specific path. `bowties2` is installed on Nargis.

best,

      Dilawar

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--
Dilawar
NCBS Bangalore

[Rikesh]

I got it working. Thanks.