Question: Issues installing bcl2fastq?
2
gravatar for a.rex
20 months ago by
a.rex180
a.rex180 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 • 4.0k views
ADD COMMENTlink modified 12 days ago by GokalpC30 • written 20 months ago by a.rex180
1

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

ADD REPLYlink written 20 months ago by cpad011211k

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

ADD REPLYlink written 20 months ago by genomax65k

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 20 months ago by a.rex180
 dpkg -L bcl2fastq

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

ADD REPLYlink written 20 months ago by cpad011211k

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 20 months ago by a.rex180

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 20 months ago • written 20 months ago by genomax65k

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

ADD REPLYlink written 20 months ago by a.rex180
1

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

ADD REPLYlink written 20 months ago by genomax65k

Did you also install boost-devel?

ADD REPLYlink written 20 months ago by ATpoint15k

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 20 months ago • written 20 months ago by a.rex180

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 20 months ago by genomax65k

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 20 months ago by a.rex180

Do you have sudo access on this machine?

ADD REPLYlink written 20 months ago by genomax65k

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 20 months ago by cpad011211k
2
gravatar for cpad0112
20 months ago by
cpad011211k
India
cpad011211k 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 20 months ago • written 20 months ago by cpad011211k

Thank you - I managed to download the deb.

ADD REPLYlink written 20 months ago by a.rex180
1
gravatar for Lina F
20 months ago by
Lina F150
Boston, MA
Lina F150 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 20 months ago by Lina F150
0
gravatar for GokalpC
3 months ago by
GokalpC30
Turkey/Ankara/Intergen
GokalpC30 wrote:

Hi

I generated deb packages and zip files for binaries for the latest 2 versions of bcl2fastq2. Feel free to try these.

All compiled on ubuntu with static library linking so there should not be any resource dependencies. Zip packages can be used on any linux distro just by adding the folder to the PATH. I tried these on Manjaro and Ubuntu so far and no issues detected. Debian packages are not converts from rpm. Fresh compiled from source code under ubuntu 18.04.

Bcl2fastq 2.19 deb package compiled via gcc 7.3

Bcl2fastq 2.20 deb package compiled via gcc 7.3

Bcl2fastq 2.20 zip package compiled via gcc 8.2

Bcl2fastq 2.20 zip package compiled via gcc 7.3

ADD COMMENTlink written 3 months ago by GokalpC30
1

Downloading something from Google Drive from a user who only just registered, on face value, looks suspicious. Can you at least provide some indication of who you are and some evidence that these packages work? We live in an age of increased cyber crime.

ADD REPLYlink written 3 months ago by Kevin Blighe41k
2

Sorry about that. I am a long time registered user in GATK forums my nickname is SkyWarrior there. I have been in bioinformatics for about 5 years and before that I was all a wetlab guy. As a hobbyist I dealt with FOSS for a long time and after I quit wetlab business as a researcher I decided to give my linux and math skills a go for bioinformatics and it has paid pretty well.

Again I am sorry if any of these links felt like a scam but believe me it is not. I am publishing the steps that I did to generate these deb files so anyone can make their of if they don't want to download but still need a private repository for themselves to keep a copy of working software.

Here are the things you need to get things up and running for this compilation to go successfully. Internet links are full of recommendations of how to get this thing done on older versions of ubuntu or other linux distro but I tried this on the latest stable and rolling ubuntu.

1- Get Ubuntu 18.04 or 18.10 running on a computer or a VM. I use VM or docker image because it is much more handy and I can keep that for later versions to build if needed. 2- Run the following commands to get your compilers and libs up to date

sudo apt-get update
sudo apt-get install gcc build-essentials libbz2-dev zlib1g-dev

These commands will install gcc 7.3 in 18.04 and gcc 8.2 in 18.10. Once these are done successfully follow the steps below.

Steps to create these deb packages your own.

  • Download the latest source code from illumina website and extract the bcl2fastq folder inside another empty folder that would keep your work tidy.

  • Once you extracted bcl2fastq folder create a folder named build next to bcl2fastq folder.

  • Now open up a terminal window inside the build folder and type the following command that is needed for proper libboost-1.54 compilation from the source code provided.

    export CPLUS_INCLUDE_PATH=/usr/include/x86_64-linux-gnu:$CPLUS_INCLUDE_PATH

This command restores the stat.h file for a missing header problem in libboost compilation.

  • Now run the below command to start the configuration.

    ../bcl2fastq/src/configure --static --prefix=/usr/local --build-type Release --package-type=deb

  • This command will go through the steps of creating static library links required to build bcl2fastq in the following step.

  • Once this command is completed successfully it is time to modify a file that prevents deb package to be generated with the proper version info successfully. Inside the build folder there is a file named CPackConfig.cmake. Open this file with a text editor and change the following line (version is for the 2.20 but you get the point.)

    SET(CPACK_PACKAGE_VERSION "v2.20.0.422") to SET(CPACK_PACKAGE_VERSION "2.20.0.422")

  • After that run the following command inside the build folder again as usual.

    make package

After these steps you should have a deb package generated successfully inside the folder build. You can use that package to install to any debian based distro.

There is also another folder named _CPack*. Inside that folder you will also find compiled binaries that can be used in any linux distro that is not compatible with deb packages.

It is sad that Illumina does not provide this by default but it is nothing impossible with a few tricks explained here.

Here are the screenshots of the running package on my Windows 10 Desktop with Ubuntu on Windows feature. It just works

bcl2fastq 2.20 deb package installed on WSL

I am preparing a video link for everyone to follow what I did visually here. Just give me an hour.

EDIT: Here is the link to the video. I just captured it. Sorry if it is not good. Quality may improve in an hour once youtube finishes its processing.

https://youtu.be/61ZkMSRJhiI

ADD REPLYlink modified 3 months ago • written 3 months ago by GokalpC30

may be you can host it on public github repos or some other version tracking public repos. gokalpceliksentegen

ADD REPLYlink written 3 months ago by cpad011211k

Can one not just use conda? Why does one need deb packages?

ADD REPLYlink written 3 months ago by RamRS21k

Sure it can be done but I had zero experience with conda package manager. In fact I wanted to have a private repository for my workplace computing environment that's why I generated these .deb packages but also noticed that there may be others in need of this software.

ADD REPLYlink written 3 months ago by GokalpC30

It's great effort on your part, but I think you could just have a specific conda channel for your workplace computing environment and save yourself some effort. I think that's what Devon Ryan does, but I could be mistaken.

ADD REPLYlink written 3 months ago by RamRS21k

it really works ,thank you

ADD REPLYlink written 9 days ago by niceeat0
0
gravatar for GokalpC
12 days ago by
GokalpC30
Turkey/Ankara/Intergen
GokalpC30 wrote:

Hi

Sorry that this is a very late reply for a repository for this build. Finally I generated a docker image for this build.

It can be had from skysbiodocker/bcl2fastq2

docker pull skysbiodocker/bcl2fastq2

There is another docker image that I used to use which is the illumina rpm build based on centos6.9 however that image is incompatible with later kernel versions especially 4.19. I also noticed that illumina rpm build of the 2.20 tool is also segfaulting under latest kernels but If you wish to use that that is also available

docker pull skysbiodocker/bcl2fastq

Beware that kernel incompatibilities may kill this image.

ADD COMMENTlink written 12 days ago by GokalpC30
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