Is it possible to provide a binary version of TPMCalculator

[xflicsu]

TPMCalculator is a useful tool to calculate expression of RNA-Seq datasets.
I try to install on our Linux system. But it failed.
So, could you provide binary version?

[r78v10a07]

Hi,
Could you, please, provide the errors you've got while compiling the tool?
Thanks,
Roberto

[xflicsu]

Hi,
Could you, please, provide the errors you've got while compiling the tool?
Thanks,
Roberto

Thanks for your response!
When I try to "make" as the installation in readme.

"make" -f nbproject/Makefile-Release.mk QMAKE= SUBPROJECTS= .build-conf
make[1]: Entering directory '/mnt/dellfs/home/lixianfeng/soft/TPMCalculator'
"make" -f nbproject/Makefile-Release.mk bin/TPMCalculator
make[2]: Entering directory '/mnt/dellfs/home/lixianfeng/soft/TPMCalculator'
mkdir -p build/Release/GNU-MacOSX/src
rm -f "build/Release/GNU-MacOSX/src/DiffExpIR.o.d"
g++ -g -I /mnt/dellfs/home/lixianfeng/soft/bamtools/include/bamtools/ -c -O2 -Iincludes -std=c++14 -MMD -MP -MF "build/Release/GNU-MacOSX/src/DiffExpIR.o.d" -o build/Release/GNU-MacOSX/src/DiffExpIR.o src/DiffExpIR.cpp
/tmp/ccP5nTfw.s: Assembler messages:
/tmp/ccP5nTfw.s:51: Error: expecting string instruction after rep' /tmp/ccP5nTfw.s:68: Error: expecting string instruction after rep'
/tmp/ccP5nTfw.s:85: Error: expecting string instruction after rep' /tmp/ccP5nTfw.s:103: Error: expecting string instruction after rep'
make[2]: *** [nbproject/Makefile-Release.mk:94: build/Release/GNU-MacOSX/src/DiffExpIR.o] Error 1
make[2]: Leaving directory '/mnt/dellfs/home/lixianfeng/soft/TPMCalculator'
make[1]: *** [nbproject/Makefile-Release.mk:85: .build-conf] Error 2
make[1]: Leaving directory '/mnt/dellfs/home/lixianfeng/soft/TPMCalculator'
make: *** [nbproject/Makefile-impl.mk:40: .build-impl] Error 2

Maybe the g++ version (7.2.0) of my linux system is not suitable to compile TPMCalculator.

[r78v10a07]

Hi,
Could you, please, send me the output of this command?

gcc --version

The easy way could be to use docker. So, you don't need to compile the code.

Thanks,
Roberto

[xflicsu]

Hi,
Could you, please, send me the output of this command?

gcc --version

The easy way could be to use docker. So, you don't need to compile the code.

Thanks,
Roberto

My system has gcc (4.4.7 default)
gcc --version
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I also change the system environment by anaconda2 with gcc 7.2.0.
./gcc --version
gcc (GCC) 7.2.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

When I compile TPMCalculator with gcc 7.2.0, I caught that error send you before.

[r78v10a07]

I was able to compile TPMCalculator with the GCC 7.2.0 in Ubuntu 17.10 using a docker image.

These are the steps I did:

Installing docker image

docker pull ubuntu:17.10
docker run -i -t ubuntu:17.10 /bin/bash
apt-get update
apt-get upgrade
apt-get install gcc g++ make git cmake libjsoncpp-dev zlib1g-dev

Installing bamtools

git clone https://github.com/pezmaster31/bamtools
cd bamtools
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=../ ..
make
make install
cd ..
export BAMTOOLS_DIR=`pwd`
export CPPFLAGS="-I $BAMTOOLS_DIR/include/bamtools/"
export LDFLAGS="-L $BAMTOOLS_DIR/lib -Wl,-rpath,$BAMTOOLS_DIR/lib"

Compiling TPMCalculator

git clone https://github.com/ncbi/TPMCalculator
cd TPMCalculator
make

GCC

root@2e5bb6a7284f:/TPMCalculator# gcc --version
gcc (Ubuntu 7.2.0-8ubuntu3.2) 7.2.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

TPMCalculator

root@2e5bb6a7284f:/TPMCalculator# ./bin/TPMCalculator

********************************************************************************

Usage: ./bin/TPMCalculator

./bin/TPMCalculator options:

-v    Print info
-h    Display this usage information.
-g    GTF file
-d    Directory with the BAM files
-b    BAM file
-k    Gene key to use from GTF file. Default: gene_id
-t    Transcript key to use from GTF file. Default: transcript_id
-c    Smaller size allowed for an intron created for genes. Default: 16. We recommend to use the reads length
-p    Use only properly paired reads. Default: No. Recommended for paired-end reads.
-q    Minimum MAPQ value to filter out reads. Default: 0. This value depends on the aligner MAPQ value.
-o    Minimum overlap between a reads and a feature. Default: 8.
-e    Extended output. This will include transcript level TPM values. Default: No.

********************************************************************************

                        Roberto Vera Alvarez, PhD
                      Emails: veraalva@ncbi.nlm.nih.gov

********************************************************************************
root@2e5bb6a7284f:/TPMCalculator# 

[r78v10a07]

I've created a static executable compiled with Ubuntu 17.10 and GCC 7.2.0.

https://github.com/ncbi/TPMCalculator/releases/tag/0.0.1

Could you, please, test it on your system?

Thanks,
Roberto

[xflicsu]

I've created a static executable compiled with Ubuntu 17.10 and GCC 7.2.0.

https://github.com/ncbi/TPMCalculator/releases/tag/0.0.1

Could you, please, test it on your system?

Thanks,
Roberto

Thanks for your help!
I test it on my system.

./TPMCalculator
FATAL: kernel too old
Aborted (core dumped)

Maybe the system version is to old.
I will try to run it on another system.