Changing the type of dynamic programming matrix element short -> int
Merge branch 'master' of ssh://git.code.sf.net/p/grasshopper-assembler/code into largedatasets
Merge branch 'master' of ssh://git.code.sf.net/p/grasshopper-assembler/code
BUGFIX in preprocessing phase (fastamerger).
Enhancement to automatically adjust the sm and gp (based on lenghth of longest read) needed in process of calculation alignment match length.
Changes to support datasets with sequences memory consumption larger than 4GB after packing. +ADDITIONAL BUG INFO
Changing debugging condition.
debug of fasta2pfasta-c
Possible hotfix for missing 1/2_noN_trimmed.fastq
Cool, that's makes sense.
Error in <grasshopper-scripts/run-grasshopper-install.sh>
Commit eddffd9751b519e22286cce265c3666014393f1f fixes the order of parameter to softlink creation to the grasshopper run script.
Modifying the installation script for root user
Compile error on Ubuntu 18.04
Compiler/MakeFile Error with CUDA
Commit 487f910d3d2e70bdf0151878bd0d12435c13a262 brings the hotfix for the issue for cuda toolkit 10.2. Appearently new toolkit introduced the problem with linking cuda kernels with g++. The issue was fixed by relying on nvcc in linkage phase.
Error in <grasshopper-scripts/run-grasshopper-install.sh>
The error is occuring in the MAKEFILE, the order of the linking statments is incorrect. For reference, I'm using Ubuntu 18.04 LTS; gcc 7.5.0; CUDA-10.2 as my system. This is the INCORRECT order as per the MAKEFILE that the compile/build proccess generates at the end of the object file list: g++ -lstdc++ -I/usr/local/cuda-10.2/include -L/usr/local/cuda-10.2/lib64 -lcudart -fopenmp -g -O2 -std=c++11 The CORRECT order is below (g++ used in VERBOSE mode) and results in proper linking: $ g++ -v -o grasshopper-build...
BUGFIX for cuda-10.2 toolkit
Compiler/MakeFile Error with CUDA
Nevermind - the issue was a very old (1.4) version of SeqAn that is installed as the default on Ubuntu 18.04. I downloaded a much newer version 2.4 from the Debian Repos and GRASShopPER compiled without the SeqAn error.
Compile error on Ubuntu 18.04
Merge branch 'master' of ssh://git.code.sf.net/p/grasshopper-assembler/code
Bugfix in correction
Adding state-size parameter to perform additional tests.
Hello Hugo, Sorry for the delay, I was defending my PhD and haven't checked the sourceforge messages. As for the seqan - as far as I know you don't really need it to be installed (compiled). It is mostly template based library so most of the implementation (and so does the functionality we use) lies in header files. To make it work just copy the library to the include folder of your system. Wojtek F.
Hello, I would really like to use grasshopper for assembling a genome!. I’m trying to install it, yet I’m failing when trying to install ‘seqan’, at least for me, none of the methods found worked (I’ve tested in several Ubuntu versions, with no luck). Any advice? B.R., MWorks Sent from Mailhttps://go.microsoft.com/fwlink/?LinkId=550986 for Windows 10
Add support of thread number from grasshopper-build parameter.
Forwarding threads number parameter from script.
Add --strip option in decompression to enforce identical paths as before tarring.
GNU tar added to dependencies.
Fork sensitivity is now double
Dataset disk space optimizations
Changing compute capability to sm30 (to support cuda10+).
Merge branch 'master' of ssh://git.code.sf.net/p/grasshopper-assembler/code
CHG: Score for different read length
CHG: run ExactScore kernel
FIX: actial -> actual
FIX: <<32 undefined behaviour
FIX: compilation errors
ADD: Gpu Zero-error matching.
rename loop variables
Part of exact algorithm
Add namespace std
ADD: log pairs before gpu
Add .idea to gitignore
Adding seqan prerequirement...
MOD: adding other sections of README file
ADD: README file with prerequirements
ADD: script to install grasshopper
ADD: script to perform compilation
ADD: main grasshopper script
RM: removing run_soap2.sh and run_sspace.sh they are now replaced with grasshopper-scripts/run-grasshopper-scaffold.sh with appropriate option.
MOD: handling no sspace in path in trimming script
ADD: script to perform scaffolding
ADD: script responsible for trimming
RM: script to run trimming is now in scripts directory
MOD: correction script gets additional warning about samtools non appearing in path
MOD: add of executables to ignore list
Merge branch 'master' of ssh://git.code.sf.net/p/grasshopper-assembler/code
ADD: Makefile for trimming executables
Add seq_len.awk, read_rename.awk
Merge branch 'master' of ssh://git.code.sf.net/p/grasshopper-assembler/code
MOD: changing the usage of grasshopper-scripts/run-grasshopper-traverse.sh
MOD: changing the usage of grasshopper-scripts/run-grasshopper-preprocess.sh
ADD: script to run traverse step
MOD: default value for smallest lexicographical index parameter
MOD: script that converts fastq to fasta became independant from input fastq names of sequences
ADD: adding git-ignores
ADD: script to run graph build
Merge branch 'master' of ssh://git.code.sf.net/p/grasshopper-assembler/code
ADD: exposing important parameters
Add scripts to run scaffolders
MOD: change the script converting fastq to fasta to fulfil FASTA format
ADD: script to run preprocess
UPDATE: removing confusing parameters in correction script comment
ADD: preprocess module
MODIFICATION: debug of correction script (removing shifts...)
ADD: scripts directory + script to run grasshopper-correct module
ADD: correcting module
ADD: Trimming module.
Traverse step add
Initial commit