configure of bcl2fastq

Question

[yueli7]

Hello,

I tried to configure bcl2fastq.

Thanks in advance for great help!

Best,

Yue

p0xxx:~/opt01/cellranger-3.1.0/bcl2fastq/src$ mkdir ../bcl2fastq-build
p0xxx:~/opt01/cellranger-3.1.0/bcl2fastq/src$ cd ../bcl2fastq-build
p0xxx:~/opt01/cellranger-3.1.0/bcl2fastq/bcl2fastq-build$ ../src/configure –prefix=/home/li/opt01/cellranger-3.1.0



-- stdint.h found as 1
-- stdlib.h found as /usr/include/stdlib.h
-- string.h found as /usr/include/string.h
-- strings.h found as /usr/include/strings.h
-- time.h found as /usr/include/time.h
-- unistd.h found as /usr/include/unistd.h
CMake Error at cmake/macros.cmake:80 (message):
Required header sys/stat.h not found.
Call Stack (most recent call first):
cmake/cxxConfigure.cmake:40 (bcl2fastq_find_header_or_die)
cxx/CMakeLists.txt:33 (include)


-- Configuring incomplete, errors occurred!
Couldn't configure the project:
/home/yli1/opt01/cellranger-3.1.0/bcl2fastq/bcl2fastq-build/bootstrap_cmake/bin/cmake -H'/home/yli1/opt01/cellranger-3.1.0/bcl2fastq/src' -B'/home/yli1/opt01/cellranger-3.1.0/bcl2fastq/bcl2fastq-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="/home/yli1/opt01/cellranger-3.1.0/bcl2fastq/src" -DBCL2FASTQ_PREFIX:PATH="/usr/local" -DBCL2FASTQ_EXEC_PREFIX:PATH="" -DCMAKE_INSTALL_PREFIX:PATH="/usr/local" -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

[swbarnes2]

Do you really not have an IT department to help you with this? When you google "Required header sys/stat.h not found.", you get an answer about making bcl2fastq. Can you explain in detail why that didn't work for you?

[yueli7]

Hello, swbarnes2,

Thank you so much for your replying.

I really do not have an IT department to help me with this.

Thank you for tell me about the I should google "Required header sys/stat.h not found."

Following is the only link I found, but I still got confusing,

Thanks in advance for your great help!

Best,

Yue

https://stackoverflow.com/questions/48717822/cmake-required-header-sys-stat-h-not-found/52266228#52266228

[Ram]

If you're on a laptop, try using conda to install whatever you need. If you're on a cluster, you will have an IT person to contact.

[yueli7]

Hello, RamRS,

Thank you so much for your kindly replying.

I am in Ubuntu 18.04.3 LTS \n \l。

Thank you again!

Best,

Yue

[Ram]

Please follow the instructions from genomax's post below.

For what it's worth, a laptop or cluster is the hardware platform you're working on. Ubuntu is the operating system. Both are important to know how to install, but the former tells us how much ownership you probably have over the computational resource.

Please invest some effort in understanding your tasks and our questions so we can help you better.

[GenoMax]

Use the directions on this page to install bcl2fastq. It covers the cmake problem you are seeing.

[yueli7]

Hello, genomax,

Thank you so much for your kindly help!

I followed https://sarahpenir.github.io/linux/Installing-bcl2fastq/.

yli1@rsch-rnk-srv01:~/opt01/cellranger-3.1.0/bcl2fastq/bcl2fastq-build$ sudo apt-get remove cmake 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Package 'cmake' is not installed, so not removed
0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.

But still comes out the same error.

Thank you again for your great help!

Best,

Yue

-- unistd.h found as /usr/include/unistd.h
CMake Error at cmake/macros.cmake:80 (message):
Required header sys/stat.h not found.
Call Stack (most recent call first):
cmake/cxxConfigure.cmake:40 (bcl2fastq_find_header_or_die)
cxx/CMakeLists.txt:33 (include)


-- Configuring incomplete, errors occurred!
Couldn't configure the project:
/home/yli1/opt01/cellranger-3.1.0/bcl2fastq/bcl2fastq-build/bootstrap_cmake/bin/cmake -H'/home/yli1/opt01/cellranger-3.1.0/bcl2fastq/src' -B'/home/yli1/opt01/cellranger-3.1.0/bcl2fastq/bcl2fastq-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="/home/yli1/opt01/cellranger-3.1.0/bcl2fastq/src" -DBCL2FASTQ_PREFIX:PATH="/usr/local" -DBCL2FASTQ_EXEC_PREFIX:PATH="" -DCMAKE_INSTALL_PREFIX:PATH="/usr/local" -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

[Ram]

The same post says what to do when the system complains about the absence of sys/stat.h. Did you try those steps?

[swbarnes2]

This is not an IT board, it's really hard for anyone not at your system to help you.

If you are a 10xGenomics customer, they have tech support that will be better at helping you.