| Patch |
File delta |
Description |
| 0002_use_debian_packaged_python joblib.patch | (download) |
assembler/src/spades_pipeline/hammer_logic.py |
11 7 + 4 - 0 !
assembler/src/spades_pipeline/lucigen_nxmate.py |
12 7 + 5 - 0 !
2 files changed, 14 insertions(+), 9 deletions(-) |
we are using debian packaged python-joblib
Debian has its own way to distinguish Python versions and there is no point
in doing this inside the code.
.
The patch is non-intrusive since it conserves the original code and uses
Debian pyyaml only if the original method fails.
|
| 0003_accept system bwa.patch | (download) |
assembler/spades.py |
22 21 + 1 - 0 !
assembler/src/spades_pipeline/support.py |
26 24 + 2 - 0 !
2 files changed, 45 insertions(+), 3 deletions(-) |
enable using debian packaged bwa instead of bwa-spades
Users might have installed a local version of bwa which is used independently
from SPAdes. This is specifically true on Debian systems where the
dependency system ensures the installation of bwa. This patch uses the
local installed bwa as fallback if bwa-spades is not found.
.
The patch is non-intrusive since it conserves the original code and uses
Debian bwa only if bwa-spades is not available.
.
Note: The duplicated which() in two files is for sure not the best solution.
In case you consider taking over the patch I'd suggest to take it over into
some common import file.
|
| 0101_cmake_ignore_removed_python yaml.patch | (download) |
assembler/ext/src/CMakeLists.txt |
2 0 + 2 - 0 !
1 file changed, 2 deletions(-) |
since we are using debian packaged python-yaml
(see 0001_use_debian_packaged_python-yaml.patch) the dir needs to be
excluded
|
| 0102_cmake_ignore_removed_python joblib.patch | (download) |
assembler/ext/src/CMakeLists.txt |
2 0 + 2 - 0 !
1 file changed, 2 deletions(-) |
since we are using debian packaged python-joblib
(see 0002_use_debian_packaged_python-joblib.patch) the dir needs to be
excluded
|
| 0103_use debian packaged bwa.patch | (download) |
assembler/ext/src/CMakeLists.txt |
1 0 + 1 - 0 !
assembler/ext/tools/CMakeLists.txt |
1 0 + 1 - 0 !
2 files changed, 2 deletions(-) |
spades originally contained a code copy of bwa since the version
of bwa which was current of the time of release did not builded with recent
gcc versions. Since this is not the case with Debian shipped bwa this code
copy is skipped.
.
See https://lists.debian.org/debian-med/2014/02/msg00192.html
.
Note: I tried to patch the Python scripts which were calling bwa-spades to
rather call /usr/bin/bwa but the test suite failed. So as an alternative
the package contains a symlink
ln -s /usr/bin/bwa /usr/lib/spades/bin/bwa-spades
which enables successful run of the test suite
|
| 0110_build_single_thread.patch | (download) |
assembler/spades_compile.sh |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
build in single thread
Upstream builds this in 8 threads, which might overwhelm weaker machines.
|
| 0114_use_debian_provided_libs.patch | (download) |
assembler/ext/src/CMakeLists.txt |
3 0 + 3 - 0 !
assembler/src/cmake/includes.cmake |
2 2 + 0 - 0 !
assembler/src/common/assembly_graph/CMakeLists.txt |
2 1 + 1 - 0 !
assembler/src/common/modules/alignment/kmer_map.hpp |
2 1 + 1 - 0 !
assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp |
2 1 + 1 - 0 !
assembler/src/common/modules/path_extend/overlap_analysis.hpp |
2 1 + 1 - 0 !
6 files changed, 6 insertions(+), 7 deletions(-) |
use more debian packaged libraries
|
| 0115_enable_compiler_messages.patch | (download) |
assembler/spades_compile.sh |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
enable compiler messages
|
| 0111_use_full_config_dirs.patch | (download) |
assembler/src/spades_pipeline/spades_logic.py |
27 27 + 0 - 0 !
1 file changed, 27 insertions(+) |
use full config include path
This patch makes sure that the config files are not dependent on local
directory structure.
|
| 0116_stable_link_order.patch | (download) |
assembler/ext/src/llvm/CMakeLists.txt |
1 1 + 0 - 0 !
1 file changed, 1 insertion(+) |
use stable sort order for file globbing
|
| 0117_build_with_debug.patch | (download) |
assembler/spades_compile.sh |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
enable building with debug symbols
|
| 0118_adjust_spades_home_again.patch | (download) |
assembler/spades_init.py |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
adjust spades_home var to install files under /usr/share/spades
|
| fix bool cast | (download) |
assembler/src/common/func/pred.hpp |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
make explicit cast to bool
|
| spelling | (download) |
assembler/manual.html |
6 3 + 3 - 0 !
assembler/src/common/assembly_graph/stats/picture_dump.hpp |
2 1 + 1 - 0 !
assembler/src/common/modules/alignment/pacbio/pac_index.hpp |
2 1 + 1 - 0 !
assembler/src/projects/hammer/hamcluster.cpp |
2 1 + 1 - 0 !
4 files changed, 6 insertions(+), 6 deletions(-) |
spelling fixes
|
| gcc7.patch | (download) |
assembler/src/common/utils/segfault_handler.hpp |
1 1 + 0 - 0 !
1 file changed, 1 insertion(+) |
fix ftbfs with gcc-7
|
| python3.patch | (download) |
assembler/changer_of_K.py |
2 1 + 1 - 0 !
assembler/spades.py |
2 1 + 1 - 0 !
assembler/spades_dev.sh |
2 1 + 1 - 0 !
assembler/spades_init.py |
2 1 + 1 - 0 !
assembler/src/projects/mts/binners/gattaca.snake |
4 2 + 2 - 0 !
assembler/src/projects/mts/mts.py |
3 1 + 2 - 0 !
assembler/src/projects/mts/multirun.py |
3 1 + 2 - 0 !
assembler/src/projects/mts/scripts/bhtsne.py |
6 3 + 3 - 0 !
assembler/src/projects/mts/scripts/bin_profiles.py |
2 1 + 1 - 0 !
assembler/src/projects/mts/scripts/choose_bins.py |
3 1 + 2 - 0 !
assembler/src/projects/mts/scripts/choose_samples.py |
3 1 + 2 - 0 !
assembler/src/projects/mts/scripts/clusters2csv.py |
3 1 + 2 - 0 !
assembler/src/projects/mts/scripts/combine_contigs.py |
3 1 + 2 - 0 !
assembler/src/projects/mts/scripts/contig_name_filter.py |
3 1 + 2 - 0 !
assembler/src/projects/mts/scripts/cut_fasta.py |
3 1 + 2 - 0 !
assembler/src/projects/mts/scripts/gather_stats.py |
3 1 + 2 - 0 !
assembler/src/projects/mts/scripts/multi_stats.py |
3 1 + 2 - 0 !
assembler/src/projects/mts/scripts/split_bins.py |
3 1 + 2 - 0 !
assembler/src/projects/mts/scripts/subsample.py |
3 1 + 2 - 0 !
assembler/src/spades_pipeline/corrector_logic.py |
2 1 + 1 - 0 !
assembler/src/spades_pipeline/easy_align.py |
2 1 + 1 - 0 !
assembler/src/spades_pipeline/hammer_logic.py |
2 1 + 1 - 0 !
assembler/src/spades_pipeline/options_storage.py |
2 1 + 1 - 0 !
assembler/src/spades_pipeline/process_cfg.py |
2 1 + 1 - 0 !
assembler/src/spades_pipeline/run_contig_breaker.py |
2 1 + 1 - 0 !
assembler/src/spades_pipeline/spades_logic.py |
6 3 + 3 - 0 !
assembler/src/spades_pipeline/support.py |
2 1 + 1 - 0 !
assembler/src/spades_pipeline/truspades/break_by_coverage.py |
2 1 + 1 - 0 !
assembler/src/spades_pipeline/truspades/generate_quality.py |
2 1 + 1 - 0 !
assembler/src/spades_pipeline/truspades/moleculo_filter_contigs.py |
2 1 + 1 - 0 !
assembler/src/spades_pipeline/truspades/reference_construction.py |
2 1 + 1 - 0 !
assembler/src/test/cap/tests/synthetic/test_generator.py |
2 1 + 1 - 0 !
assembler/src/test/teamcity/deprecated/bh_ecoli_1k.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/deprecated/bh_ecoli_mda_lane1.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/deprecated/full_run.sh |
19 6 + 13 - 0 !
assembler/src/test/teamcity/deprecated/spades_mc_bfaecium_ant.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/deprecated/spades_mc_is220.sh |
5 2 + 3 - 0 !
assembler/src/test/teamcity/deprecated/spades_mc_is220_1k.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/deprecated/spades_mc_is220_1k_ant.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/deprecated/spades_mc_is480.sh |
5 2 + 3 - 0 !
assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7_pre.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/deprecated/spades_sc_lane1.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/deprecated/spades_sc_lane1_full.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/deprecated/spades_sc_mruber.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/deprecated/spades_sc_mruber_pre.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/deprecated/spades_sc_phepa.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/deprecated/spades_sc_phepa_pre.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/deprecated/spades_sc_pmarinus.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/deprecated/spades_sc_saureus_lane7.sh |
4 2 + 2 - 0 !
assembler/src/test/teamcity/teamcity.py |
4 2 + 2 - 0 !
assembler/src/test/teamcity/update_threshold.py |
4 2 + 2 - 0 !
assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh |
4 2 + 2 - 0 !
assembler/src/tools/clean_contaminations/16SrRNA/taxonomy.sh |
2 1 + 1 - 0 !
assembler/src/tools/clean_contaminations/clean_contam_by_index_id.sh |
6 3 + 3 - 0 !
assembler/src/tools/cleancontigs/cleancontigs.py |
2 1 + 1 - 0 !
assembler/src/tools/cleancontigs/sort_contigs.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/analyze_sinks.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/break_scaffolds_into_contigs.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/compare_fasta.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/compare_gaps.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/compare_gaps_pos.py |
3 1 + 2 - 0 !
assembler/src/tools/contig_analysis/compare_runs.sh |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/compare_used_snps.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/gap_finder.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/get_misassembled_contigs.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/texify_results.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/visualizer/main.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/visualizer/mis_parser.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/visualizer/misassemblies.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/visualizer/misassemblies_old.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/visualizer/miss_nocov.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/visualizer/parser.py |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/visualizer/run_parser.sh |
2 1 + 1 - 0 !
assembler/src/tools/contig_analysis/visualizer/run_viz.sh |
4 2 + 2 - 0 !
assembler/src/tools/dataset_hammer |
2 1 + 1 - 0 !
assembler/src/tools/dataset_tar |
2 1 + 1 - 0 !
assembler/src/tools/estimation/run_real.sh |
3 2 + 1 - 0 !
assembler/src/tools/estimation_deprecated/Nx_plot.py |
5 3 + 2 - 0 !
assembler/src/tools/estimation_deprecated/README |
2 1 + 1 - 0 !
assembler/src/tools/loc_pic.py |
2 1 + 1 - 0 !
assembler/src/tools/misc/assembler_runner/runner.py |
2 1 + 1 - 0 !
assembler/src/tools/misc/copyrighter.py |
2 1 + 1 - 0 !
assembler/src/tools/misc/datasets_converter.py |
2 1 + 1 - 0 !
assembler/src/tools/misc/datasets_info2yaml_converter.py |
2 1 + 1 - 0 !
assembler/src/tools/misc/datasets_info_cleaner.py |
2 1 + 1 - 0 !
assembler/src/tools/misc/gcc_version_check.py |
2 1 + 1 - 0 !
assembler/src/tools/misc/sam_analysis_sorter.py |
2 1 + 1 - 0 !
assembler/src/tools/misc/sam_analyzer_2.py |
2 1 + 1 - 0 !
assembler/src/tools/misc/sv_simulator.py |
2 1 + 1 - 0 !
assembler/src/tools/misc/txt2gff.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/crop/crop_bfaecium.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/crop/crop_genome.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/crop/paired_crop.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/ideal_by_fasta.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/paired_reads_quality.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/reads_quality.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/stat/coverage.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/stat/coverage_hist.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/stat/is.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/stat/raw.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/stat/raws_w_orientation.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/stat/shift.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/stat/single_log_to_paired.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/stat/trim.py |
2 1 + 1 - 0 !
assembler/src/tools/res_counter/run.pl |
2 1 + 1 - 0 !
assembler/src/tools/spades_download_stats/filter.py |
2 1 + 1 - 0 !
assembler/src/tools/spades_pipeline/spades_download_binary.py |
2 1 + 1 - 0 !
assembler/src/tools/truseq/quast_all.py |
2 1 + 1 - 0 !
assembler/src/tools/truseq/quast_all.sh |
2 1 + 1 - 0 !
assembler/truspades.py |
6 3 + 3 - 0 !
111 files changed, 149 insertions(+), 169 deletions(-) |
make sure python3 interpreter is used in scripts
|
| yaml_load.patch | (download) |
assembler/spades.py |
10 5 + 5 - 0 !
assembler/src/spades_pipeline/corrector_logic.py |
2 1 + 1 - 0 !
assembler/src/spades_pipeline/hammer_logic.py |
4 2 + 2 - 0 !
assembler/src/spades_pipeline/spades_logic.py |
2 1 + 1 - 0 !
assembler/src/tools/reads_utils/reads_quality.py |
2 1 + 1 - 0 !
5 files changed, 10 insertions(+), 10 deletions(-) |
specify yaml loader
see https://github.com/yaml/pyyaml/wiki/PyYAML-yaml.load(input)-Deprecation
|
