Answers.Body: <p>Install it with conda.</p>
  <pre><code>conda install -c dranew bcl2fastq
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-06-25T13:34:48.880Z
Answers.Text: Hope you don't get sued by Illumina for illegal distribution of their software...
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-06-25T15:19:43.323Z
Answers.Text: ... need to preferably install Anaconda3/minicoda .
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-06-25T13:32:19.867Z
Answers.LastActivityDate: 2020-06-25T13:32:19.867Z
Answers.UserDisplayName: Mike
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-06-22T06:17:52.907Z
Answers.Text: The OP is running the software on their own Ubuntu machine, I'm not sure EasyBuild would be appropriate in context.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-06-22T05:29:41.553Z
Answers.LastActivityDate: 2020-06-22T05:29:41.553Z
Answers.UserDisplayName: Sethos II
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-06T16:24:09.950Z
Comments.Text: 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`?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-06T17:58:46.553Z
Comments.Text: 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?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-06T18:17:58.493Z
Comments.Text: 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.
Comments.UserDisplayName: Lou_A
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-06T18:22:41.157Z
Comments.Text: 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.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-06T18:27:06.993Z
Comments.Text: 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.
Comments.UserDisplayName: Lou_A
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-06T18:34:23.383Z
Comments.Text: Still too long, so I'll attach a txt file.
Comments.UserDisplayName: Lou_A
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-06T18:38:26.240Z
Comments.Text: Let us [continue this discussion in chat](https://chat.stackexchange.com/rooms/94603/discussion-between-l-aparicio-and-terdon).
Comments.UserDisplayName: Lou_A
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-06T18:38:43.280Z
Comments.Text: Just add the last few lines, that's all we need. And did you install build essential?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-06T19:00:05.893Z
Comments.Text: I did add the build-essential
Comments.UserDisplayName: Lou_A
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-06T20:11:54.627Z
Comments.Text: 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.
Comments.UserDisplayName: Lou_A
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-06T22:50:04.447Z
Comments.Text: 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.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-07T09:40:40.537Z
Comments.Text: 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).
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-07T12:10:20.797Z
Comments.Text: Thanks. It certainly looks that way.
Comments.UserDisplayName: Lou_A
Tags: <software-installation>
Title: bcl2fastq2 v2.20.0 converstion software on Ubuntu 18.04
ThreadText: # 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-username_1).  
  > **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.  
  
  ---
  
  