Activity for grasshopper

  • Wojciech Frohmberg committed [ddef28]

    Changing the type of dynamic programming matrix element short -> int

  • Wojciech Frohmberg committed [6398ad]

    Merge branch 'master' of ssh://git.code.sf.net/p/grasshopper-assembler/code into largedatasets

  • Wojtek Frohmberg committed [77e034]

    Merge branch 'master' of ssh://git.code.sf.net/p/grasshopper-assembler/code

  • Wojtek Frohmberg committed [8c10cc]

    BUGFIX in preprocessing phase (fastamerger).

  • Wojtek Frohmberg committed [378024]

    Enhancement to automatically adjust the sm and gp (based on lenghth of longest read) needed in process of calculation alignment match length.

  • Wojciech Frohmberg committed [e50a32]

    Changes to support datasets with sequences memory consumption larger than 4GB after packing. +ADDITIONAL BUG INFO

  • Wojtek Frohmberg committed [a467df]

    Changing debugging condition.

  • Wojtek Frohmberg committed [d50d2b]

    debug of fasta2pfasta-c

  • Wojtek Frohmberg committed [89d1ec]

    Possible hotfix for missing 1/2_noN_trimmed.fastq

  • cement_head cement_head posted a comment on ticket #2

    Cool, that's makes sense.

  • Wojciech Frohmberg Wojciech Frohmberg modified ticket #3

    Error in <grasshopper-scripts/run-grasshopper-install.sh>

  • Wojciech Frohmberg Wojciech Frohmberg posted a comment on ticket #3

    Commit eddffd9751b519e22286cce265c3666014393f1f fixes the order of parameter to softlink creation to the grasshopper run script.

  • Wojtek Frohmberg committed [eddffd]

    Modifying the installation script for root user

  • Wojciech Frohmberg Wojciech Frohmberg modified ticket #1

    Compile error on Ubuntu 18.04

  • Wojciech Frohmberg Wojciech Frohmberg modified ticket #2

    Compiler/MakeFile Error with CUDA

  • Wojciech Frohmberg Wojciech Frohmberg posted a comment on ticket #2

    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.

  • cement_head cement_head created ticket #3

    Error in <grasshopper-scripts/run-grasshopper-install.sh>

  • cement_head cement_head posted a comment on ticket #2

    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...

  • Wojtek Frohmberg committed [487f91]

    BUGFIX for cuda-10.2 toolkit

  • cement_head cement_head created ticket #2

    Compiler/MakeFile Error with CUDA

  • cement_head cement_head posted a comment on ticket #1

    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.

  • cement_head cement_head created ticket #1

    Compile error on Ubuntu 18.04

  • Wojciech Frohmberg committed [100010]

    Merge branch 'master' of ssh://git.code.sf.net/p/grasshopper-assembler/code

  • Wojciech Frohmberg committed [2afba5]

    Bugfix in correction

  • Wojciech Frohmberg committed [e38e45]

    Adding state-size parameter to perform additional tests.

  • Wojciech Frohmberg Wojciech Frohmberg posted a comment on discussion General Discussion

    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.

  • Hugo Mauricio Peña Mercado Hugo Mauricio Peña Mercado posted a comment on discussion General Discussion

    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

  • Wojciech Frohmberg committed [9cfe0d]

    Add support of thread number from grasshopper-build parameter.

  • Wojciech Frohmberg committed [3e1217]

    Forwarding threads number parameter from script.

  • Wojciech Frohmberg committed [9d73e3]

    Add --strip option in decompression to enforce identical paths as before tarring.

  • Wojciech Frohmberg committed [bc3096]

    GNU tar added to dependencies.

  • Wojciech Frohmberg committed [5949ea]

    Fork sensitivity is now double

  • Wojciech Frohmberg committed [075e5d]

    Dataset disk space optimizations

  • Wojciech Frohmberg committed [74f2e1]

    Changing compute capability to sm30 (to support cuda10+).

  • Wojciech Frohmberg committed [c67cb5]

    Merge branch 'master' of ssh://git.code.sf.net/p/grasshopper-assembler/code

  • Jan Badura Jan Badura committed [1ac1f8]

    CHG: Score for different read length

  • Jan Badura Jan Badura committed [553f65]

    CHG: run ExactScore kernel

  • Jan Badura Jan Badura committed [05b50b]

    FIX: actial -> actual

  • Jan Badura Jan Badura committed [67f652]

    FIX: <<32 undefined behaviour

  • Jan Badura Jan Badura committed [5cecbf]

    FIX: compilation errors

  • Artur Laskowski Artur Laskowski committed [11fb5a]

    ADD: Gpu Zero-error matching.

  • Jan Badura Jan Badura committed [6bd2a2]

    rename loop variables

  • Jan Badura Jan Badura committed [2222be]

    Part of exact algorithm

  • Jan Badura Jan Badura committed [7512db]

    Add namespace std

  • Jan Badura Jan Badura committed [adf7c1]

    ADD: log pairs before gpu

  • Jan Badura Jan Badura committed [f2f45b]

    Add .idea to gitignore

  • Wojciech Frohmberg committed [476062]

    Adding seqan prerequirement...

  • Wojciech Frohmberg committed [08843b]

    MOD: adding other sections of README file

  • Wojciech Frohmberg committed [0398b2]

    ADD: README file with prerequirements

  • Wojciech Frohmberg committed [cf7213]

    ADD: script to install grasshopper

  • Wojciech Frohmberg committed [ed9e91]

    ADD: script to perform compilation

  • Wojciech Frohmberg committed [b785d6]

    ADD: main grasshopper script

  • Wojciech Frohmberg committed [e8c5ee]

    RM: removing run_soap2.sh and run_sspace.sh they are now replaced with grasshopper-scripts/run-grasshopper-scaffold.sh with appropriate option.

  • Wojciech Frohmberg committed [22b81f]

    MOD: handling no sspace in path in trimming script

  • Wojciech Frohmberg committed [b16106]

    ADD: script to perform scaffolding

  • Wojciech Frohmberg committed [76a832]

    ADD: script responsible for trimming

  • Wojciech Frohmberg committed [8703e7]

    RM: script to run trimming is now in scripts directory

  • Wojciech Frohmberg committed [f32c48]

    MOD: correction script gets additional warning about samtools non appearing in path

  • Wojciech Frohmberg committed [57c4e4]

    MOD: add of executables to ignore list

  • Wojciech Frohmberg committed [577e3a]

    Merge branch 'master' of ssh://git.code.sf.net/p/grasshopper-assembler/code

  • Wojciech Frohmberg committed [39b5a7]

    ADD: Makefile for trimming executables

  • Jan Badura Jan Badura committed [f40cf1]

    Add seq_len.awk, read_rename.awk

  • Jan Badura Jan Badura committed [92e7f1]

    Merge branch 'master' of ssh://git.code.sf.net/p/grasshopper-assembler/code

  • Wojciech Frohmberg committed [83e718]

    MOD: changing the usage of grasshopper-scripts/run-grasshopper-traverse.sh

  • Wojciech Frohmberg committed [47b82d]

    MOD: changing the usage of grasshopper-scripts/run-grasshopper-preprocess.sh

  • Wojciech Frohmberg committed [681944]

    ADD: script to run traverse step

  • Wojciech Frohmberg committed [9d7195]

    MOD: default value for smallest lexicographical index parameter

  • Wojciech Frohmberg committed [c5e493]

    MOD: script that converts fastq to fasta became independant from input fastq names of sequences

  • Wojciech Frohmberg committed [f18076]

    ADD: adding git-ignores

  • Wojciech Frohmberg committed [c0f72c]

    ADD: script to run graph build

  • Wojciech Frohmberg committed [8f1fd1]

    Merge branch 'master' of ssh://git.code.sf.net/p/grasshopper-assembler/code

  • Wojciech Frohmberg committed [e316e5]

    ADD: exposing important parameters

  • Jan Badura Jan Badura committed [6535d6]

    Add scripts to run scaffolders

  • Wojciech Frohmberg committed [303478]

    MOD: change the script converting fastq to fasta to fulfil FASTA format

  • Wojciech Frohmberg committed [ea0d16]

    ADD: script to run preprocess

  • Wojciech Frohmberg committed [18cf53]

    UPDATE: removing confusing parameters in correction script comment

  • Wojciech Frohmberg committed [231e0f]

    ADD: preprocess module

  • Wojciech Frohmberg committed [38f886]

    MODIFICATION: debug of correction script (removing shifts...)

  • Wojciech Frohmberg committed [7f5499]

    ADD: scripts directory + script to run grasshopper-correct module

  • Wojciech Frohmberg committed [a5b595]

    ADD: correcting module

  • Artur Laskowski Artur Laskowski committed [dbc5c5]

    ADD: Trimming module.

  • Wojciech Frohmberg committed [0e86fa]

    Traverse step add

  • Wojciech Frohmberg committed [3ab888]

    Initial commit

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