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Xingyu-Liao / LongRepMarker_v2.0

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Installation error #9

Open evo-eco-gen opened 2 years ago

evo-eco-gen commented 2 years ago

Hi, Trying to install on a different machine (Ubuntu 20.04.1; all dependencies successfully installed through conda, inc gcc 10.3).

I get:

03)Installing gfatools. gfatools installation failed, please check the installation log [ /home/kozakk/bin/LongRepMarker_v2.1.2-master/log/paf2gfa_Install.log ].

gfatools_warning.log says:

In file included from main.c:1: /usr/include/stdlib.h:25:10: fatal error: bits/libc-header-start.h: No such file or directory 25 | #include <bits/libc-header-start.h> | ^~~~~~ compilation terminated. make: *** [Makefile:19: main.o] Error 1

gfatools_Install.log:

gcc -c -g -Wall -Wc++-compat -std=c99 -O2 -I. main.c -o main.o

I have no idea what to make of this -I imagine some header somewhere needs to be changed?

Xingyu-Liao commented 2 years ago

Hi, Trying to install on a different machine (Ubuntu 20.04.1; all dependencies successfully installed through conda, inc gcc 10.3).

I get:

03)Installing gfatools. gfatools installation failed, please check the installation log [ /home/kozakk/bin/LongRepMarker_v2.1.2-master/log/paf2gfa_Install.log ].

gfatools_warning.log says:

In file included from main.c:1: /usr/include/stdlib.h:25:10: fatal error: bits/libc-header-start.h: No such file or directory 25 | #include <bits/libc-header-start.h> | ^~~~~~ compilation terminated. make: *** [Makefile:19: main.o] Error 1

gfatools_Install.log:

gcc -c -g -Wall -Wc++-compat -std=c99 -O2 -I. main.c -o main.o

I have no idea what to make of this -I imagine some header somewhere needs to be changed?

Hi,

Sorry to reply to you late. We have mentioned the solution to this problem in FAQs section of the README page (https://github.com/Xingyu-Liao/LongRepMarker_v2.0). Please review the content displayed in the following figure.

image

Thank you again!

Best,

Xingyu Liao

evo-eco-gen commented 2 years ago

Hi,

No worries, thanks a lot for getting back. I installed gcc-multilib, upgraded everything else on the system (Ubuntu 20.04), and rebooted. Sam e problem continues, except now it appears one step later: 03)Installing gfatools. gfatools installation failed, please check the installation log [ /media/data1/bin/LongRepMarker_v2.1.2-master/log/paf2gfa_Install.log ].

paf2gfa_Install.log: gcc -c -g -Wall -Wc++-compat -std=c99 -O2 -I.. misc.c -o misc.o

paf2gfa_Warning.log: In file included from main.c:1: /usr/include/stdlib.h:25:10: fatal error: bits/libc-header-start.h: No such file or directory 25 | #include <bits/libc-header-start.h> | ^~~~~~ compilation terminated. make: *** [Makefile:19: main.o] Error 1

Xingyu-Liao commented 2 years ago

Hi,

No worries, thanks a lot for getting back. I installed gcc-multilib, upgraded everything else on the system (Ubuntu 20.04), and rebooted. Sam e problem continues, except now it appears one step later: 03)Installing gfatools. gfatools installation failed, please check the installation log [ /media/data1/bin/LongRepMarker_v2.1.2-master/log/paf2gfa_Install.log ].

paf2gfa_Install.log: gcc -c -g -Wall -Wc++-compat -std=c99 -O2 -I.. misc.c -o misc.o

paf2gfa_Warning.log: In file included from main.c:1: /usr/include/stdlib.h:25:10: fatal error: bits/libc-header-start.h: No such file or directory 25 | #include <bits/libc-header-start.h> | ^~~~~~ compilation terminated. make: *** [Makefile:19: main.o] Error 1

Hi,

In fact, paf2gfa and bcftools tools are useless in the detection mode you selected, so there is no need to install them. Please copy the following text to replace the content in the Makefile.sh（~/LongRepMarker_v2.1.2-master/Makefile.sh）, and rebuild the LongRepMarker tool.

!/bin/bash

alignment_dir=./alignment program_dir=./programs read_dir=./readfile result_dir=./results log_dir=./log bin_dir=./bin if [ -d $CONDA_PREFIX ]; then export C_INCLUDE_PATH=$C_INCLUDE_PATH:/usr/include:$CONDA_PREFIX/include fi

Remove folders

rm -rf ./alignment rm -rf ./readfile rm -rf ./results rm -rf ./programs rm -rf ./Nanopore rm -rf ./log rm -rf ./pycache

Mkdir

mkdir ./alignment mkdir ./readfile mkdir ./results mkdir ./programs mkdir ./log

Check

echo "-------------------------------------------------------------------------------" echo "01)Checking foundation." which unzip || { echo "unzip is not found"; exit 1; } echo "unzip is ok." which gcc || { echo "java is not found"; exit 1; } echo "gcc is ok." which java || { echo "java is not found"; exit 1; } echo "java is ok." which python || { echo "python is not found"; exit 1; } echo "python is ok." which perl || { echo "perl is not found"; exit 1; } echo "perl is ok." which cmake || { echo "cmake is not found"; exit 1; } echo "cmake is ok."

Unzip-dsk

rm -rf ./programs/scripts rm -rf ./programs/corePrograms mkdir ./programs/scripts mkdir ./programs/corePrograms cp ./tools/scripts/dsk ./programs/scripts/ cp ./tools/scripts/dsk2ascii ./programs/scripts/ cp ./tools/scripts/karect ./programs/scripts/

Unzip-RepeatMasker

rm -rf ./programs/RepeatMasker unzip -o -d ./programs/ ./tools/RepeatMasker.zip > ./tools/unzip_RepeatMasker.log mv ./tools/unzip_RepeatMasker.log ./log/

Unzip-RMblast

rm -rf ./programs/rmblast-2.11.0 unzip -o -d ./programs/ ./tools/rmblast-2.11.0.zip > ./tools/unzip_RMblast.log mv ./tools/unzip_RMblast.log ./log/

Unzip-Classifier

rm -rf ./programs/Classifier unzip -o -d ./programs/ ./tools/Classifier.zip > ./tools/unzip_classifier.log mv ./tools/unzip_classifier.log ./log/

Unzip-necat

rm -rf ./programs/necat unzip -o -d ./programs/ ./tools/necat.zip > ./tools/unzip_necat.log mv ./tools/unzip_necat.log ./log/

Unzip-TRF

rm -rf ./programs/TRF-master unzip -o -d ./programs/ ./tools/TRF-master.zip > ./tools/unzip_TRF.log mv ./tools/unzip_TRF.log ./log/

Unzip-cdhit

rm -rf ./programs/cdhit-master unzip -o -d ./programs/ ./tools/cdhit-master.zip > ./tools/unzip_cdhit.log mv ./tools/unzip_cdhit.log ./log/

Unzip-gfatools

rm -rf ./programs/gfatools-master unzip -o -d ./programs/ ./tools/gfatools-master.zip > ./tools/unzip_gfatools.log mv ./tools/unzip_gfatools.log ./log/

Unzip-htslib

rm -rf ./programs/htslib-1.14 tar -jxvf ./tools/htslib-1.14.tar.bz2 -C ./programs/ > ./tools/unzip_htslib.log mv ./tools/unzip_htslib.log ./log/

Unzip-bcftools

rm -rf ./programs/bcftools-1.14 tar -jxvf ./tools/bcftools-1.14.tar.bz2 -C ./programs/ > ./tools/unzip_bcftools.log mv ./tools/unzip_bcftools.log ./log/

Edit permission

chmod 777 -R ./programs chmod 777 -R ./alignment chmod 777 -R ./readfile chmod 777 -R ./log chmod 777 -R ./results chmod 777 -R ./tools

Install-dsk

echo "-------------------------------------------------------------------------------" echo "02)Installing the dependent scripts." echo "Dependent scripts are installed." echo "[Location]: "$(pwd)"/programs/scripts" echo "-------------------------------------------------------------------------------" echo "03)Installing cdhit." cd ./programs/cdhit-master/ make MAX_SEQ=100000000 1> ./cdhit_Install.log 2> ./cdhit_Warning.log cd .. cd .. mv ./programs/cdhit-master/cdhit_Install.log ./log/ mv ./programs/cdhit-master/cdhit_Warning.log ./log/ cdhitFile=$(pwd)"/programs/cdhit-master/cd-hit-est" if [[ -f "$cdhitFile" ]]; then echo "cd-hit is installed." echo "[Location]: "$(pwd)"/programs/cdhit-master" else echo "cd-hit installation failed, please check the installation log [" $(pwd)"/log/cdhit_Install.log ]." exit 1; fi echo "-------------------------------------------------------------------------------" echo "04)Installing rmblast." echo $(pwd)"/programs/rmblast-2.11.0" echo "RMblast is installed." echo "-------------------------------------------------------------------------------" echo "05)Installing TRF." cd ./programs/TRF-master ./configure 1> ./TRF_Configure.log 2> ./TRF_Configure_Warning.log make DESTDIR=./programs/TRF-master 1> ./TRF_Install.log 2> ./TRF_Install_Warning.log make install DESTDIR=./programs/TRF-master 1> ./TRF_Install.log 2> ./TRF_Install_Warning.log cd .. cd .. mv ./programs/TRF-master/TRF_Install.log ./log/ mv ./programs/TRF-master/TRF_Install_Warning.log ./log/ mv ./programs/TRF-master/TRF_Configure.log ./log/ mv ./programs/TRF-master/TRF_Configure_Warning.log ./log/ TRFFile=$(pwd)"/programs/TRF-master/build/src/trf" if [[ -f "$TRFFile" ]]; then echo "TRF is installed." echo "[Location]: "$(pwd)"/programs/TRF-master" else echo "TRF installation failed, please check the installation log [" $(pwd)"/log/TRF_Install.log ]." exit 1; fi echo "-------------------------------------------------------------------------------" echo "06)Installing RepeatMasker." echo "RepeatMasker is installed." echo "[Location]: "$(pwd)"/programs/RepeatMasker" echo "-------------------------------------------------------------------------------" echo "07)Installing Classifier." echo "Classifier is installed." echo "[Location]: "$(pwd)"/programs/Classifier" echo "-------------------------------------------------------------------------------"

mkdir_log

if [ ! -d $log_dir ] then mkdir $log_dir fi

mkdir_read

if [ ! -d $read_dir ] then mkdir $read_dir fi

mkdir_result

if [ ! -d $result_dir ] then mkdir $result_dir fi

mkdir_alignment

if [ ! -d $alignment_dir ] then mkdir $alignment_dir fi echo "10)Compiling java programs." rm -rf ./.class rm -rf ./.py rm -rf ./.pyc cd ./tools/src rm -rf ./.class javac CommonClass.java javac AlignmentThreads.java javac CoreModules.java javac LongRepMarker.java javac TimMemCheck.java javac threadTimMem.java javac threadTRF.java javac threadLTRlong.java javac threadLTR.java javac threadRepeatCut.java javac LongRepMarker.java chmod 777 -R ./. cd .. cd .. cp ./tools/src/.py ./ mv ./tools/src/.class ./ echo $(pwd)"/programs/" echo "All java programs are compiled." echo "[Location]: "$(pwd)"/" echo "-------------------------------------------------------------------------------" echo " "

Edit permission

chmod 777 -R ./programs chmod 777 -R ./alignment chmod 777 -R ./readfile chmod 777 -R ./log chmod 777 -R ./results echo "LongRepMarker_v2.1.2 has been sucessfully installed. Thanks!" echo " "

evo-eco-gen commented 2 years ago

The reference mode problem was a different question. Here I am trying to get an installation working on another machine to run the mode with raw PB reads. Does that not require paf2gfa? (Since nothing worked for me right away, I have tried to get either mode to work.)

Xingyu-Liao commented 2 years ago

The reference mode problem was a different question. Here I am trying to get an installation working on another machine to run the mode with raw PB reads. Does that not require paf2gfa? (Since nothing worked for me right away, I have tried to get either mode to work.)

Hi,

The paf2gfa and bcftools are only used in detection mode based on only long reads. If you don't need to use this mode, there is no need to install these two tools. In addition, the detection mode based on only long reads is in the process of upgrading, and it cannot be used normally at present. I apologize for the inconvenience caused by the upgrade.

Best,

Xingyu Liao

evo-eco-gen commented 2 years ago

Hi,

Ok, I understand about the long read mode. I did want to use it, but it is not essential.

Thanks for the new makefile. It (almost) worked: I had to add * in lines 182 and 185-6. Below is the modified code, which now works fine for me.

!/bin/bash

alignment_dir=./alignment program_dir=./programs read_dir=./readfile result_dir=./results log_dir=./log bin_dir=./bin if [ -d $CONDA_PREFIX ]; then export C_INCLUDE_PATH=$C_INCLUDE_PATH:/usr/include:$CONDA_PREFIX/include fi

Remove folders

rm -rf ./alignment rm -rf ./readfile rm -rf ./results rm -rf ./programs rm -rf ./Nanopore rm -rf ./log rm -rf ./pycarm -rf ./pycache__

Mkdir

mkdir ./alignment mkdir ./readfile mkdir ./results mkdir ./programs mkdir ./log

Check

echo "-------------------------------------------------------------------------------" echo "01)Checking foundation." which unzip || { echo "unzip is not found"; exit 1; } echo "unzip is ok." which gcc || { echo "java is not found"; exit 1; } echo "gcc is ok." which java || { echo "java is not found"; exit 1; } echo "java is ok." which python || { echo "python is not found"; exit 1; } echo "python is ok." which perl || { echo "perl is not found"; exit 1; } echo "perl is ok." which cmake || { echo "cmake is not found"; exit 1; } echo "cmake is ok."

Unzip-dsk

rm -rf ./programs/scripts rm -rf ./programs/corePrograms mkdir ./programs/scripts mkdir ./programs/corePrograms cp ./tools/scripts/dsk ./programs/scripts/ cp ./tools/scripts/dsk2ascii ./programs/scripts/ cp ./tools/scripts/karect ./programs/scripts/

Unzip-RepeatMasker

rm -rf ./programs/RepeatMasker unzip -o -d ./programs/ ./tools/RepeatMasker.zip > ./tools/unzip_RepeatMasker.log mv ./tools/unzip_RepeatMasker.log ./log/

Unzip-RMblast

rm -rf ./programs/rmblast-2.11.0 unzip -o -d ./programs/ ./tools/rmblast-2.11.0.zip > ./tools/unzip_RMblast.log mv ./tools/unzip_RMblast.log ./log/

Unzip-Classifier

rm -rf ./programs/Classifier unzip -o -d ./programs/ ./tools/Classifier.zip > ./tools/unzip_classifier.log mv ./tools/unzip_classifier.log ./log/

Unzip-necat

rm -rf ./programs/necat unzip -o -d ./programs/ ./tools/necat.zip > ./tools/unzip_necat.log mv ./tools/unzip_necat.log ./log/

Unzip-TRF

rm -rf ./programs/TRF-master unzip -o -d ./programs/ ./tools/TRF-master.zip > ./tools/unzip_TRF.log mv ./tools/unzip_TRF.log ./log/

Unzip-cdhit

rm -rf ./programs/cdhit-master unzip -o -d ./programs/ ./tools/cdhit-master.zip > ./tools/unzip_cdhit.log mv ./tools/unzip_cdhit.log ./log/

Unzip-gfatools

rm -rf ./programs/gfatools-master unzip -o -d ./programs/ ./tools/gfatools-master.zip > ./tools/unzip_gfatools.log mv ./tools/unzip_gfatools.log ./log/

Unzip-htslib

rm -rf ./programs/htslib-1.14 tar -jxvf ./tools/htslib-1.14.tar.bz2 -C ./programs/ > ./tools/unzip_htslib.log mv ./tools/unzip_htslib.log ./log/

Unzip-bcftools

rm -rf ./programs/bcftools-1.14 tar -jxvf ./tools/bcftools-1.14.tar.bz2 -C ./programs/ > ./tools/unzip_bcftools.log mv ./tools/unzip_bcftools.log ./log/

Edit permission

chmod 777 -R ./programs chmod 777 -R ./alignment chmod 777 -R ./readfile chmod 777 -R ./log chmod 777 -R ./results chmod 777 -R ./tools

Install-dsk

echo "-------------------------------------------------------------------------------" echo "02)Installing the dependent scripts." echo "Dependent scripts are installed." echo "[Location]: "$(pwd)"/programs/scripts" echo "-------------------------------------------------------------------------------" echo "03)Installing cdhit." cd ./programs/cdhit-master/ make MAX_SEQ=100000000 1> ./cdhit_Install.log 2> ./cdhit_Warning.log cd .. cd .. mv ./programs/cdhit-master/cdhit_Install.log ./log/ mv ./programs/cdhit-master/cdhit_Warning.log ./log/ cdhitFile=$(pwd)"/programs/cdhit-master/cd-hit-est" if [[ -f "$cdhitFile" ]]; then echo "cd-hit is installed." echo "[Location]: "$(pwd)"/programs/cdhit-master" else echo "cd-hit installation failed, please check the installation log [" $(pwd)"/log/cdhit_Install.log ]." exit 1; fi echo "-------------------------------------------------------------------------------" echo "04)Installing rmblast." echo $(pwd)"/programs/rmblast-2.11.0" echo "RMblast is installed." echo "-------------------------------------------------------------------------------" echo "05)Installing TRF." cd ./programs/TRF-master ./configure 1> ./TRF_Configure.log 2> ./TRF_Configure_Warning.log make DESTDIR=./programs/TRF-master 1> ./TRF_Install.log 2> ./TRF_Install_Warning.log make install DESTDIR=./programs/TRF-master 1> ./TRF_Install.log 2> ./TRF_Install_Warning.log cd .. cd .. mv ./programs/TRF-master/TRF_Install.log ./log/ mv ./programs/TRF-master/TRF_Install_Warning.log ./log/ mv ./programs/TRF-master/TRF_Configure.log ./log/ mv ./programs/TRF-master/TRF_Configure_Warning.log ./log/ TRFFile=$(pwd)"/programs/TRF-master/build/src/trf" if [[ -f "$TRFFile" ]]; then echo "TRF is installed." echo "[Location]: "$(pwd)"/programs/TRF-master" else echo "TRF installation failed, please check the installation log [" $(pwd)"/log/TRF_Install.log ]." exit 1; fi echo "-------------------------------------------------------------------------------" echo "06)Installing RepeatMasker." echo "RepeatMasker is installed." echo "[Location]: "$(pwd)"/programs/RepeatMasker" echo "-------------------------------------------------------------------------------" echo "07)Installing Classifier." echo "Classifier is installed." echo "[Location]: "$(pwd)"/programs/Classifier" echo "-------------------------------------------------------------------------------"

mkdir_log

if [ ! -d $log_dir ] then mkdir $log_dir fi

mkdir_read

if [ ! -d $read_dir ] then mkdir $read_dir fi

mkdir_result

if [ ! -d $result_dir ] then mkdir $result_dir fi

mkdir_alignment

if [ ! -d $alignment_dir ] then mkdir $alignment_dir fi echo "10)Compiling java programs." rm -rf ./.class rm -rf ./.py rm -rf ./.pyc cd ./tools/src rm -rf ./.class javac CommonClass.java javac AlignmentThreads.java javac CoreModules.java javac LongRepMarker.java javac TimMemCheck.java javac threadTimMem.java javac threadTRF.java javac threadLTRlong.java javac threadLTR.java javac threadRepeatCut.java javac LongRepMarker.java chmod 777 -R ./. cd .. cd .. cp ./tools/src/.py ./ mv ./tools/src/.class ./ echo $(pwd)"/programs/" echo "All java programs are compiled." echo "[Location]: "$(pwd)"/" echo "-------------------------------------------------------------------------------" echo " "

Edit permission

chmod 777 -R ./programs chmod 777 -R ./alignment chmod 777 -R ./readfile chmod 777 -R ./log chmod 777 -R ./results echo "LongRepMarker_v2.1.2 has been sucessfully installed. Thanks!" echo " "