Comments (7)
Hi,
Could you, please, provide the errors you've got while compiling the tool?
Thanks,
Roberto
from tpmcalculator.
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.
from tpmcalculator.
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
from tpmcalculator.
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.
from tpmcalculator.
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: [email protected]
********************************************************************************
root@2e5bb6a7284f:/TPMCalculator#
from tpmcalculator.
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
from tpmcalculator.
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.
from tpmcalculator.
Related Issues (20)
- Gene number in input GTF differs from the TPMCalculator output HOT 3
- symbol lookup error HOT 9
- Sets the name of the output HOT 2
- Add a new option to use a directory as output destination HOT 1
- For the paired end reads, is it recommended to use option -p or should i go with default without it? HOT 1
- Output file description HOT 2
- /usr/bin/ld: cannot find -lbamtools HOT 2
- *_genes.out duplicate genes HOT 3
- Compilation error: collect2: error: ld returned 1 exit status HOT 2
- Is the read counting strand-specific? HOT 2
- Key ID for gene name was not found on GTF line HOT 3
- No TPM values, no reads processed HOT 9
- Chromosome with name: ENST.... does not exist HOT 10
- Output files desctiption HOT 1
- Installation without docker HOT 1
- Meaning of "UniqueReads" in genes.out file? HOT 2
- Possible to use gff3 in TPMCalculator v 0.4? HOT 1
- Build problems on Ubuntu and MacOSX HOT 1
- Help me please HOT 1
- After installing version 0.0.4, -version still prints 0.0.3
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