Question: Issues installing bcl2fastq?
2
gravatar for a.rex
4 months ago by
a.rex90
a.rex90 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 • 613 views
ADD COMMENTlink modified 8 weeks ago by Biostar ♦♦ 20 • written 4 months ago by a.rex90
1

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

ADD REPLYlink written 4 months ago by cpad01123.6k

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

ADD REPLYlink written 4 months ago by genomax39k

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 4 months ago by a.rex90
 dpkg -L bcl2fastq

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

ADD REPLYlink written 4 months ago by cpad01123.6k

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 4 months ago by a.rex90

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 4 months ago • written 4 months ago by genomax39k

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

ADD REPLYlink written 4 months ago by a.rex90
1

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

ADD REPLYlink written 4 months ago by genomax39k

Did you also install boost-devel?

ADD REPLYlink written 4 months ago by ATPoint2.6k

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 4 months ago • written 4 months ago by a.rex90

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 4 months ago by genomax39k

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 4 months ago by a.rex90

Do you have sudo access on this machine?

ADD REPLYlink written 4 months ago by genomax39k

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 4 months ago by cpad01123.6k
2
gravatar for cpad0112
4 months ago by
cpad01123.6k
cpad01123.6k 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 4 months ago • written 4 months ago by cpad01123.6k

Thank you - I managed to download the deb.

ADD REPLYlink written 4 months ago by a.rex90
1
gravatar for Lina F
4 months 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 4 months ago by Lina F110
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 990 users visited in the last hour