<p>Install it with conda.</p>
<pre><code>conda install -c dranew bcl2fastq
</code></pre>

CC BY-SA 4.0
2020-06-25T13:34:48.880Z
Hope you don't get sued by Illumina for illegal distribution of their software...
Devon Ryan
CC BY-SA 4.0
2020-06-25T15:19:43.323Z
... need to preferably install Anaconda3/minicoda .
M__
CC BY-SA 4.0
2020-06-25T13:32:19.867Z
2020-06-25T13:32:19.867Z
Mike
<p>Where are you running the software? In general and especially for servers and high performance clusters I would recommend to use a module system like <a href="https://github.com/TACC/Lmod" rel="nofollow noreferrer">Lmod</a> in conjunction with <a href="https://github.com/easybuilders/easybuild" rel="nofollow noreferrer">EasyBuild</a>, which contains configs for <a href="https://github.com/easybuilders/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/b/bcl2fastq2" rel="nofollow noreferrer">bcl2fastq2</a> that take care of the installation. A module system allows you to use different versions and to keep your environment clean among other benefits.</p>

CC BY-SA 4.0
2020-06-22T06:17:52.907Z
The OP is running the software on their own Ubuntu machine, I'm not sure EasyBuild would be appropriate in context.
M__
CC BY-SA 4.0
2020-06-22T05:29:41.553Z
2020-06-22T05:29:41.553Z
Sethos II
<p>bcl2fastq is a program that converts Illumina run output from .bcl to fastq. I'm having difficulties installing the software I downloaded from Illumina on my Ubuntu 18.04. I've followed their installation manual, but the software is not building when I enter the command "make".  I receive the error message... "make: *** No targets specified and no makefile found. Stop. Has anyone had similar experience? Is there another software that will install easier on Ubuntu?</p>

<p>Software:
<a href="https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html" rel="nofollow noreferrer">https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html</a></p>

<p>Manual:
<a href="https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf" rel="nofollow noreferrer">https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf</a></p>

<p>Steps followed:</p>

<pre><code>export TMP=/tmp
export SOURCE=<span class="math-container">${TMP}/bcl2fastq
export BUILD=$</span>{TMP}/bcl2fastq2-v2.20.0-build
export INSTALL_DIR=/usr/local/bcl2fastq2-v2.20.0

cd ${TMP}
tar -xvzf bcl2fastq2-v2.20.0.499-Source.tar.gz

mkdir <span class="math-container">${BUILD}
cd $</span>{BUILD}
chmod ugo+x <span class="math-container">${SOURCE}/src/configure
chmod ugo+x $</span>{SOURCE}/src/cmake/bootstrap/installCmake.sh
<span class="math-container">${SOURCE}/src/configure --prefix=$</span>{INSTALL_DIR}

cd ${BUILD}
make
</code></pre>

<p>The final command is supposed to be <code>make install</code>, but the <code>configure</code> step fails with:</p>

<pre><code>[ . . . ]
-- Configuring incomplete, errors occurred! 
Couldn't configure the project: 
/tmp/bcl2fastq2-v2.20.0-build/bootstrap_cmake/bin/cmake -H'/tmp/bcl2fastq/src' -B'/tmp/bcl2fastq2-v2.20.0-build' -G'Unix Makefiles' -DBCL2FASTQ_NAME_SHORT:STRING="bcl2fastq" -DBCL2FASTQ_NAME_LONG:STRING="BCL to FASTQ file converter" -DBCL2FASTQ_COPYRIGHT:STRING="Copyright (c) 2007-2017 Illumina, Inc." -DBCL2FASTQ_VERSION_MAJOR:STRING="2" -DBCL2FASTQ_VERSION_MINOR:STRING="20" -DBCL2FASTQ_VERSION_PATCH:STRING="0" -DBCL2FASTQ_VERSION_BUILD:STRING="422" -DBCL2FASTQ_VERSION:STRING="2.20.0.422" -DBCL2FASTQ_SOURCE_DIR:STRING="/tmp/bcl2fastq/src" -DBCL2FASTQ_PREFIX:PATH="/usr/local/bcl2fastq2-v2.20.0" -DBCL2FASTQ_EXEC_PREFIX:PATH="" -DCMAKE_INSTALL_PREFIX:PATH="/usr/local/bcl2fastq2-v2.20.0" -DBCL2FASTQ_BINDIR:PATH="" -DBCL2FASTQ_LIBDIR:PATH="" -DBCL2FASTQ_LIBEXECDIR:PATH="" -DBCL2FASTQ_INCLUDEDIR:PATH="" -DBCL2FASTQ_DATADIR:PATH="" -DBCL2FASTQ_DOCDIR:PATH="" -DBCL2FASTQ_MANDIR:PATH="" -DCMAKE_BUILD_TYPE:STRING="RelWithDebInfo" -DCMAKE_PARALLEL:STRING="1" 
Moving CMakeCache.txt to CMakeCache.txt.removed 
</code></pre>

CC BY-SA 4.0
2019-06-06T16:24:09.950Z
Please [edit] your question and add: i) the URL of the software you downloaded; ii) the exactly commands you have run. Are you running `make` from the directory where you have run `.configure`? Did you run `configure`?
terdon
CC BY-SA 4.0
2019-06-06T17:58:46.553Z
Thanks for the edit, that's clearer! Now, some of those commands should have given an error message, did they? Especially the `${SOURCE}/src/configure --prefix=${INSTALL_DIR}`, did that finish successfully? And what happens if you now run `cd /tmp/bcl2fastq2-v2.20.0-build; make`? Have you installed the `build-essentials` (`sudo apt install build-essentials`) package on Ubuntu?
terdon
CC BY-SA 4.0
2019-06-06T18:17:58.493Z
No errors displayed when I ran the commands.  I haven't been able to install the build-essentials... I get the message "Unable to locate package build-essentials.  The message I get when I run "make" is something about not having a target.
Lou_A
CC BY-SA 4.0
2019-06-06T18:22:41.157Z
please run configure again and show us the output. There should be a message there telling you what's missing. And sorry, that should have been `sudo apt  install build-essential`, no final s.
terdon
CC BY-SA 4.0
2019-06-06T18:27:06.993Z
I'm seeing the errors at the bottom.  I'm attaching a screenshot.  The screenshot is too long, so I'll add them in three parts.
Lou_A
CC BY-SA 4.0
2019-06-06T18:34:23.383Z
Still too long, so I'll attach a txt file.
Lou_A
CC BY-SA 4.0
2019-06-06T18:38:26.240Z
Let us [continue this discussion in chat](https://chat.stackexchange.com/rooms/94603/discussion-between-l-aparicio-and-terdon).
Lou_A
CC BY-SA 4.0
2019-06-06T18:38:43.280Z
Just add the last few lines, that's all we need. And did you install build essential?
terdon
CC BY-SA 4.0
2019-06-06T19:00:05.893Z
I did add the build-essential
Lou_A
CC BY-SA 4.0
2019-06-06T20:11:54.627Z
So, I started the process over and I get the error when I run "make"  

laparic1@crb-byphhv2:/tmp/bcl2fastq2-v2.20.0-build$ cd ${BUILD}
laparic1@crb-byphhv2:/tmp/bcl2fastq2-v2.20.0-build$ make
make: *** No targets specified and no makefile found.  Stop.

I wonder if I the command before it, cd ${BUILD}, is correct because I'm already in the BUILD directory.
Lou_A
CC BY-SA 4.0
2019-06-06T22:50:04.447Z
Please ***[edit]*** your question and add all this information. You can use the [formatting tools](https://bioinformatics.stackexchange.com/help/formatting) to format your commands and their output as code. Comments are hard to read, easy to miss and can be deleted without warning.
terdon
CC BY-SA 4.0
2019-06-07T09:40:40.537Z
I suggest you install it via the RPM, this is an incredibly annoying package to compile yourself (this is unfortunately common with software from Illumina).
Devon Ryan
CC BY-SA 4.0
2019-06-07T12:10:20.797Z
Thanks. It certainly looks that way.
Lou_A
<software-installation>
bcl2fastq2 v2.20.0 converstion software on Ubuntu 18.04
# bcl2fastq2 v2.20.0 converstion software on Ubuntu 18.04

(Asked by: username_0 on 2019-06-06)

bcl2fastq is a program that converts Illumina run output from .bcl to fastq. I'm having difficulties installing the software I downloaded from Illumina on my Ubuntu 18.04. I've followed their installation manual, but the software is not building when I enter the command "make".  I receive the error message... "make: *** No targets specified and no makefile found. Stop. Has anyone had similar experience? Is there another software that will install easier on Ubuntu?
Software:
https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html
Manual:
https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf
Steps followed:
export TMP=/tmp
export SOURCE=${TMP}/bcl2fastq
export BUILD=${TMP}/bcl2fastq2-v2.20.0-build
export INSTALL_DIR=/usr/local/bcl2fastq2-v2.20.0

cd ${TMP}
tar -xvzf bcl2fastq2-v2.20.0.499-Source.tar.gz

mkdir ${BUILD}
cd ${BUILD}
chmod ugo+x ${SOURCE}/src/configure
chmod ugo+x ${SOURCE}/src/cmake/bootstrap/installCmake.sh
${SOURCE}/src/configure --prefix=${INSTALL_DIR}

cd ${BUILD}
make

The final command is supposed to be make install, but the configure step fails with:
[ . . . ]
-- Configuring incomplete, errors occurred! 
Couldn't configure the project: 
/tmp/bcl2fastq2-v2.20.0-build/bootstrap_cmake/bin/cmake -H'/tmp/bcl2fastq/src' -B'/tmp/bcl2fastq2-v2.20.0-build' -G'Unix Makefiles' -DBCL2FASTQ_NAME_SHORT:STRING="bcl2fastq" -DBCL2FASTQ_NAME_LONG:STRING="BCL to FASTQ file converter" -DBCL2FASTQ_COPYRIGHT:STRING="Copyright (c) 2007-2017 Illumina, Inc." -DBCL2FASTQ_VERSION_MAJOR:STRING="2" -DBCL2FASTQ_VERSION_MINOR:STRING="20" -DBCL2FASTQ_VERSION_PATCH:STRING="0" -DBCL2FASTQ_VERSION_BUILD:STRING="422" -DBCL2FASTQ_VERSION:STRING="2.20.0.422" -DBCL2FASTQ_SOURCE_DIR:STRING="/tmp/bcl2fastq/src" -DBCL2FASTQ_PREFIX:PATH="/usr/local/bcl2fastq2-v2.20.0" -DBCL2FASTQ_EXEC_PREFIX:PATH="" -DCMAKE_INSTALL_PREFIX:PATH="/usr/local/bcl2fastq2-v2.20.0" -DBCL2FASTQ_BINDIR:PATH="" -DBCL2FASTQ_LIBDIR:PATH="" -DBCL2FASTQ_LIBEXECDIR:PATH="" -DBCL2FASTQ_INCLUDEDIR:PATH="" -DBCL2FASTQ_DATADIR:PATH="" -DBCL2FASTQ_DOCDIR:PATH="" -DBCL2FASTQ_MANDIR:PATH="" -DCMAKE_BUILD_TYPE:STRING="RelWithDebInfo" -DCMAKE_PARALLEL:STRING="1" 
Moving CMakeCache.txt to CMakeCache.txt.removed

**Tags:** software-installation
> **Comments:**
> **username_1**: Please [edit] your question and add: i) the URL of the software you downloaded; ii) the exactly commands you have run. Are you running `make` from the directory where you have run `.configure`? Did you run `configure`?  
> **username_1**: Thanks for the edit, that's clearer! Now, some of those commands should have given an error message, did they? Especially the `${SOURCE}/src/configure --prefix=${INSTALL_DIR}`, did that finish successfully? And what happens if you now run `cd /tmp/bcl2fastq2-v2.20.0-build; make`? Have you installed the `build-essentials` (`sudo apt install build-essentials`) package on Ubuntu?  
> **username_0**: No errors displayed when I ran the commands.  I haven't been able to install the build-essentials... I get the message "Unable to locate package build-essentials.  The message I get when I run "make" is something about not having a target.  
> **username_1**: please run configure again and show us the output. There should be a message there telling you what's missing. And sorry, that should have been `sudo apt  install build-essential`, no final s.  
> **username_0**: I'm seeing the errors at the bottom.  I'm attaching a screenshot.  The screenshot is too long, so I'll add them in three parts.  
> **username_0**: Still too long, so I'll attach a txt file.  
> **username_0**: Let us [continue this discussion in chat](https://chat.stackexchange.com/rooms/94603/discussion-between-l-aparicio-and-terdon).  
> **username_1**: Just add the last few lines, that's all we need. And did you install build essential?  
> **username_0**: I did add the build-essential  
> **username_0**: So, I started the process over and I get the error when I run "make"    laparic1@crb-byphhv2:/tmp/bcl2fastq2-v2.20.0-build$ cd ${BUILD} laparic1@crb-byphhv2:/tmp/bcl2fastq2-v2.20.0-build$ make make: *** No targets specified and no makefile found.  Stop.  I wonder if I the command before it, cd ${BUILD}, is correct because I'm already in the BUILD directory.  
> **username_1**: Please ***[edit]*** your question and add all this information. You can use the [formatting tools](https://bioinformatics.stackexchange.com/help/formatting) to format your commands and their output as code. Comments are hard to read, easy to miss and can be deleted without warning.  
> **username_2**: I suggest you install it via the RPM, this is an incredibly annoying package to compile yourself (this is unfortunately common with software from Illumina).  
> **username_0**: Thanks. It certainly looks that way.  

---

## 2 answers

### Answer by username_3 on 2020-06-25. Score: 4

Install it with conda.
conda install -c dranew bcl2fastq

> **Comments:**
> **username_2**: Hope you don't get sued by Illumina for illegal distribution of their software...  
> **username_4**: ... need to preferably install Anaconda3/minicoda .  

---

### Answer by username_5 on 2020-06-22. Score: 0

Where are you running the software? In general and especially for servers and high performance clusters I would recommend to use a module system like [Lmod](https://github.com/TACC/Lmod) in conjunction with [EasyBuild](https://github.com/easybuilders/easybuild), which contains configs for [bcl2fastq2](https://github.com/easybuilders/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/b/bcl2fastq2) that take care of the installation. A module system allows you to use different versions and to keep your environment clean among other benefits.

> **Comments:**
> **username_4**: The OP is running the software on their own Ubuntu machine, I'm not sure EasyBuild would be appropriate in context.  

---

