Question: Issues installing bcl2fastq?
2
gravatar for a.rex
9 weeks ago by
a.rex80
a.rex80 wrote:

I am trying to install bcl2fastq from source.

However, during the make process, I am encountering an error:

make[2]: * [c++/lib/demultiplex/CMakeFiles/casava_demultiplex.dir/BclDemultiplexer.cpp.o] Error 1 make[1]: [c++/lib/demultiplex/CMakeFiles/casava_demultiplex.dir/all] Error 2 make: ** [all] Error 2

Does anyone know how you can get around this, and what this means? I have built the boost that comes with the redist folder and have pointed to this when configuring the bcl2fastq program.

demultiplexing bcl2fastq • 418 views
ADD COMMENTlink modified 3 days ago by Biostar ♦♦ 20 • written 9 weeks ago by a.rex80
1

you can download bcl2fastaq deb from https://github.com/igorbarinov/bcl2fastq. Try the deb

ADD REPLYlink written 9 weeks ago by cpad01122.2k

Software linked here is older version (should work unless the data is from NovaSeq).

ADD REPLYlink written 9 weeks ago by genomax34k

Thanks for this, I downloaded the deb, and used sudo dpkg -i bcl2fastq_1.8.4-2_amd64-2.deb. Where does it install to?

ADD REPLYlink written 9 weeks ago by a.rex80
 dpkg -L bcl2fastq

Should give you where each file went. In general, it should be available in your path :)

ADD REPLYlink written 9 weeks ago by cpad01122.2k

Unfortunately I need the v2 version for a next-seq. When I convert to deb with alien, I get the following error which I cannot diagnose. dpkg-deb: error: parsing file 'debian/bcl2fastq2/DEBIAN/control' near line 2 package 'bcl2fastq2': error in Version string 'v2.17.1.14-2': version number does not start with a digit dh_builddeb: dpkg-deb --build debian/bcl2fastq2 .. returned exit code 2 make: * [binary-arch] Error 1 Any ideas would be helpful...

ADD REPLYlink written 9 weeks ago by a.rex80

Why did you download v.1.8.4? v.2.17 (as a .deb) is also available at the link @cpad0112 posted.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by genomax34k

I downloaded the deb for 1.8.4. 2.17 is only available as an rpm file....I think.

ADD REPLYlink written 9 weeks ago by a.rex80
1

My bad (dyslexia kicked in). You should follow the other set of directions from @cpad0112 then: C: Issues installing bcl2fastq? .

ADD REPLYlink written 9 weeks ago by genomax34k

Did you also install boost-devel?

ADD REPLYlink written 9 weeks ago by ATPoint1.6k

Hello. Yes, I did this after unzipping the boost-1.44 in the redist folder:

sudo apt-get update
sudo apt-get install build-essential g++ python-dev autotools-dev libicu-dev build-essential libbz2-dev libboost-all-dev
./bootstrap.sh 
./bjam 
sudo ./bjam install.
ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by a.rex80

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

If you are able to, use the .rpm Illumina provides instead.

ADD REPLYlink written 9 weeks ago by genomax34k

Hi, I tried using rpm. However, if I follow the illumina installation guide I also get an error when using the command: rpm --install bcl2fastq2-v2.18.0.12-Linux-x86_64.rpm. It says: rpm: RPM should not be used directly install RPM packages, use Alien instead! rpm: However assuming you know what you are doing... error: Failed dependencies: /bin/sh is needed by bcl2fastq2-v2.18.0.12-1.x86_64

ADD REPLYlink written 9 weeks ago by a.rex80

Do you have sudo access on this machine?

ADD REPLYlink written 9 weeks ago by genomax34k

Install alien. Alien package will convert rpm to deb based on certain architecture assumption. read https://wiki.debian.org/Alien. In general it would install, but some times, it (converted deb) may fail.

ADD REPLYlink written 9 weeks ago by cpad01122.2k
2
gravatar for cpad0112
9 weeks ago by
cpad01122.2k
cpad01122.2k wrote:

Please download bcl2fastq2-v2.17.1.14-Linux-x86_64.rpm from above link and follow the instructions below: (copy/pasted from: https://github.com/igorbarinov/bcl2fastq/blob/master/install-2.17.sh)

 sudo apt-get install alien --assume-yes
 sudo alien bcl2fastq2-v2.17.1.14-Linux-x86_64.rpm
  sudo dpkg -i bcl2fastq2_0v2.17.1.14-2_amd64.deb

I was able to generate deb (bcl2fastq2_0v2.17.1.14-2_amd64.deb) and install it. Let us know if you are not able to generate deb. bcl2fastq is available in /usr/local/bin.

my system:

$ cat /etc/lsb-release 
DISTRIB_ID=LinuxMint
DISTRIB_RELEASE=18.2
DISTRIB_CODENAME=sonya
DISTRIB_DESCRIPTION="Linux Mint 18.2 Sonya

Linux mint 18.2 is based on ubuntu xenial (16.0.4)

$ uname -a
Linux genomics 4.8.0-53-generic #56~16.04.1-Ubuntu SMP Tue May 16 01:18:56 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

For some reason, if you fail to generate deb, i can upload the deb file and share a link to download.

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by cpad01122.2k

Thank you - I managed to download the deb.

ADD REPLYlink written 9 weeks ago by a.rex80
1
gravatar for Lina F
9 weeks ago by
Lina F110
Boston, MA
Lina F110 wrote:

I took some notes last time I installed bcl2fastq and this worked for me on Ubuntu. However, it's an older version, so feel free to modify:

SOURCE_NAME=bcl2fastq2-v2.17.1.14.tar.zip
SOURCE_URL=ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/$SOURCE_NAME
SOURCE_WORKDIR=/tmp/bcl2fastq

sudo apt-get update && \
    apt-get install -y build-essential libboost1.54-all-dev cmake zlibc libc6 unzip wget && \

$SOURCE_WORKDIR
cd $SOURCE_WORKDIR && \
    wget $SOURCE_URL 
cd $SOURCE_WORKDIR && unzip $SOURCE_NAME && \
    tar xzf $(basename $SOURCE_NAME .zip).gz && \
    mkdir $SOURCE_WORKDIR/bcl2fastq/build && \
    cd $SOURCE_WORKDIR/bcl2fastq/build && \
    ../src/configure --prefix=/usr/local && \
    make && \
    make install
ADD COMMENTlink written 9 weeks ago by Lina F110
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