BOL: Related items

Installing croSSRoad on Ubuntu !

ComBioX — Fri, 29 May 2026 05:19:45 -0500

(base) hp@hp-HP-Z2-Tower-G9-Workstation-Desktop-PC:~/jitendraTEST$ conda
usage: conda [-h] [-v] [--no-plugins] [-V] COMMAND ...

conda is a tool for managing and deploying applications, environments and packages.

options:
-h, --help Show this help message and exit.
-v, --verbose Can be used multiple times. Once for detailed output, twice for INFO logging, thrice for DEBUG logging, four times for TRACE logging.
--no-plugins Disable all plugins that are not built into conda.
-V, --version Show the conda version number and exit.

commands:
The following built-in and plugins subcommands are available.

COMMAND
activate Activate a conda environment.
clean Remove unused packages and caches.
commands List all available conda subcommands (including those from plugins). Generally only used by tab-completion.
compare Compare packages between conda environments.
config Modify configuration values in .condarc.
create Create a new conda environment from a list of specified packages.
deactivate Deactivate the current active conda environment.
doctor Display a health report for your environment.
env Create and manage conda environments.
export Export a given environment
info Display information about current conda install.
init Initialize conda for shell interaction.
install Install a list of packages into a specified conda environment.
list List installed packages in a conda environment.
notices Retrieve latest channel notifications.
package Create low-level conda packages. (EXPERIMENTAL)
remove (uninstall) Remove a list of packages from a specified conda environment.
rename Rename an existing environment.
repoquery Advanced search for repodata.
run Run an executable in a conda environment.
search Search for packages and display associated information using the MatchSpec format.
update (upgrade) Update conda packages to the latest compatible version.
(base) hp@hp-HP-Z2-Tower-G9-Workstation-Desktop-PC:~/jitendraTEST$ conda create -n jitENV
Retrieving notices: done
Channels:
- ursky
- bioconda
- conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 25.7.0
latest version: 26.5.0

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /home/hp/miniforge3/envs/jitENV

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate jitENV
#
# To deactivate an active environment, use
#
# $ conda deactivate

(base) hp@hp-HP-Z2-Tower-G9-Workstation-Desktop-PC:~/jitendraTEST$ conda activate jitENV
(jitENV) hp@hp-HP-Z2-Tower-G9-Workstation-Desktop-PC:~/jitendraTEST$ conda install conda-forge::mamba
Channels:
- ursky
- bioconda
- conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 25.7.0
latest version: 26.5.0

Please update conda by running

$ conda update -n base -c conda-forge conda

## Package Plan ##

environment location: /home/hp/miniforge3/envs/jitENV

added / updated specs:
- conda-forge::mamba

The following packages will be downloaded:

package | build
---------------------------|-----------------
ca-certificates-2026.5.20 | hbd8a1cb_0 127 KB conda-forge
cpp-expected-1.3.1 | h171cf75_0 24 KB conda-forge
fmt-12.1.0 | hff5e90c_0 193 KB conda-forge
libarchive-3.8.7 | gpl_hc2c16d8_101 869 KB conda-forge
libcurl-8.20.0 | hcf29cc6_0 458 KB conda-forge
libgcc-15.2.0 | he0feb66_19 1017 KB conda-forge
libgcc-ng-15.2.0 | h69a702a_19 27 KB conda-forge
libgomp-15.2.0 | he0feb66_19 590 KB conda-forge
libmamba-2.6.2 | hd28c85e_0 2.7 MB conda-forge
libmsgpack-c-6.1.0 | h54a6638_6 39 KB conda-forge
libsolv-0.7.38 | h9463b59_0 509 KB conda-forge
libstdcxx-15.2.0 | h934c35e_19 5.6 MB conda-forge
libxml2-2.15.3 | h49c6c72_0 46 KB conda-forge
libxml2-16-2.15.3 | hca6bf5a_0 547 KB conda-forge
mamba-2.6.2 | hce6dcdd_0 553 KB conda-forge
ncurses-6.6 | hdb14827_0 897 KB conda-forge
nlohmann_json-abi-3.12.0 | h0f90c79_1 4 KB conda-forge
reproc-14.2.7.post0 | hb03c661_1 35 KB conda-forge
reproc-cpp-14.2.7.post0 | hecca717_1 26 KB conda-forge
simdjson-4.6.4 | hb700be7_0 310 KB conda-forge
spdlog-1.17.0 | hab81395_1 192 KB conda-forge
------------------------------------------------------------
Total: 14.6 MB

The following NEW packages will be INSTALLED:

_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-20_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-hda65f42_9
c-ares conda-forge/linux-64::c-ares-1.34.6-hb03c661_0
ca-certificates conda-forge/noarch::ca-certificates-2026.5.20-hbd8a1cb_0
cpp-expected conda-forge/linux-64::cpp-expected-1.3.1-h171cf75_0
fmt conda-forge/linux-64::fmt-12.1.0-hff5e90c_0
icu conda-forge/linux-64::icu-78.3-h33c6efd_0
keyutils conda-forge/linux-64::keyutils-1.6.3-hb9d3cd8_0
krb5 conda-forge/linux-64::krb5-1.22.2-ha1258a1_0
libarchive conda-forge/linux-64::libarchive-3.8.7-gpl_hc2c16d8_101
libcurl conda-forge/linux-64::libcurl-8.20.0-hcf29cc6_0
libedit conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0
libev conda-forge/linux-64::libev-4.33-hd590300_2
libgcc conda-forge/linux-64::libgcc-15.2.0-he0feb66_19
libgcc-ng conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_19
libgomp conda-forge/linux-64::libgomp-15.2.0-he0feb66_19
libiconv conda-forge/linux-64::libiconv-1.18-h3b78370_2
liblzma conda-forge/linux-64::liblzma-5.8.3-hb03c661_0
libmamba conda-forge/linux-64::libmamba-2.6.2-hd28c85e_0
libmsgpack-c conda-forge/linux-64::libmsgpack-c-6.1.0-h54a6638_6
libnghttp2 conda-forge/linux-64::libnghttp2-1.68.1-h877daf1_0
libsolv conda-forge/linux-64::libsolv-0.7.38-h9463b59_0
libssh2 conda-forge/linux-64::libssh2-1.11.1-hcf80075_0
libstdcxx conda-forge/linux-64::libstdcxx-15.2.0-h934c35e_19
libxml2 conda-forge/linux-64::libxml2-2.15.3-h49c6c72_0
libxml2-16 conda-forge/linux-64::libxml2-16-2.15.3-hca6bf5a_0
libzlib conda-forge/linux-64::libzlib-1.3.2-h25fd6f3_2
lz4-c conda-forge/linux-64::lz4-c-1.10.0-h5888daf_1
lzo conda-forge/linux-64::lzo-2.10-h280c20c_1002
mamba conda-forge/linux-64::mamba-2.6.2-hce6dcdd_0
ncurses conda-forge/linux-64::ncurses-6.6-hdb14827_0
nlohmann_json-abi conda-forge/noarch::nlohmann_json-abi-3.12.0-h0f90c79_1
openssl conda-forge/linux-64::openssl-3.6.2-h35e630c_0
reproc conda-forge/linux-64::reproc-14.2.7.post0-hb03c661_1
reproc-cpp conda-forge/linux-64::reproc-cpp-14.2.7.post0-hecca717_1
simdjson conda-forge/linux-64::simdjson-4.6.4-hb700be7_0
spdlog conda-forge/linux-64::spdlog-1.17.0-hab81395_1
yaml-cpp conda-forge/linux-64::yaml-cpp-0.8.0-h3f2d84a_0
zstd conda-forge/linux-64::zstd-1.5.7-hb78ec9c_6

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(jitENV) hp@hp-HP-Z2-Tower-G9-Workstation-Desktop-PC:~/jitendraTEST$ mamba install -c jitendralab -c bioconda -c conda-forge crossroad -y
jitendralab/noarch ??.?MB @ ??.?MB/s 0.3s
jitendralab/linux-64 ??.?MB @ ??.?MB/s 0.4s
bioconda/linux-64 5.6MB @ 2.9MB/s 1.9s
bioconda/noarch 5.6MB @ 2.5MB/s 2.2s
conda-forge/noarch 26.4MB @ 6.0MB/s 4.5s
conda-forge/linux-64 53.8MB @ 6.7MB/s 8.2s

Transaction

Prefix: /home/hp/miniforge3/envs/jitENV

Updating specs:

- crossroad

Package Version Build Channel Size
─────────────────────────────────────────────────────────────────────────────────────────────────
Install:
─────────────────────────────────────────────────────────────────────────────────────────────────

+ annotated-doc 0.0.4 pyhcf101f3_0 conda-forge Cached
+ annotated-types 0.7.0 pyhd8ed1ab_1 conda-forge Cached
+ anyio 4.13.0 pyhcf101f3_0 conda-forge 147kB
+ argcomplete 3.6.3 pyhd8ed1ab_0 conda-forge Cached
+ aws-c-auth 0.10.3 h3aafcba_1 conda-forge 134kB
+ aws-c-cal 0.9.14 h8e43964_1 conda-forge 57kB
+ aws-c-common 0.13.1 hb03c661_0 conda-forge 242kB
+ aws-c-compression 0.3.2 h16e98cb_1 conda-forge 22kB
+ aws-c-event-stream 0.7.1 h9be7a74_1 conda-forge 59kB
+ aws-c-http 0.11.0 hcbcd92d_1 conda-forge 230kB
+ aws-c-io 0.26.3 h955231c_3 conda-forge 182kB
+ aws-c-mqtt 0.15.2 h8af55cf_3 conda-forge 222kB
+ aws-c-s3 0.12.3 h00bea6e_2 conda-forge 153kB
+ aws-c-sdkutils 0.2.4 h16e98cb_5 conda-forge 59kB
+ aws-checksums 0.2.10 h16e98cb_1 conda-forge 102kB
+ aws-crt-cpp 0.38.3 h7b0d4b4_2 conda-forge 413kB
+ aws-sdk-cpp 1.11.747 h5a171d8_5 conda-forge 4MB
+ azure-core-cpp 1.16.2 h206d751_0 conda-forge 349kB
+ azure-identity-cpp 1.13.3 hed0cdb0_1 conda-forge 251kB
+ azure-storage-blobs-cpp 12.17.0 hf824e48_1 conda-forge 587kB
+ azure-storage-common-cpp 12.13.0 ha7a2c86_0 conda-forge 159kB
+ azure-storage-files-datalake-cpp 12.15.0 h1e5b466_0 conda-forge 304kB
+ backports.zstd 1.5.0 py314h680f03e_0 conda-forge 8kB
+ bedtools 2.31.1 h13024bc_3 bioconda Cached
+ biopython 1.87 py314h5bd0f2a_0 conda-forge 3MB
+ brotli 1.2.0 hed03a55_1 conda-forge Cached
+ brotli-bin 1.2.0 hb03c661_1 conda-forge Cached
+ brotli-python 1.2.0 py314h3de4e8d_1 conda-forge 367kB
+ certifi 2026.5.20 pyhd8ed1ab_0 conda-forge 134kB
+ charset-normalizer 3.4.7 pyhd8ed1ab_0 conda-forge Cached
+ click 8.4.1 pyhc90fa1f_0 conda-forge 105kB
+ colorama 0.4.6 pyhd8ed1ab_1 conda-forge Cached
+ contourpy 1.3.3 py314h97ea11e_4 conda-forge 324kB
+ crossroad 0.3.6 pyh7e60211_0 jitendralab 2MB
+ cycler 0.12.1 pyhcf101f3_2 conda-forge Cached
+ dnspython 2.8.0 pyhcf101f3_0 conda-forge Cached
+ email-validator 2.3.0 pyhd8ed1ab_0 conda-forge 47kB
+ email_validator 2.3.0 hd8ed1ab_0 conda-forge 7kB
+ exceptiongroup 1.3.1 pyhd8ed1ab_0 conda-forge Cached
+ expat 2.8.1 hecca717_0 conda-forge 148kB
+ fastapi 0.136.3 h5ddb490_0 conda-forge 5kB
+ fastapi-cli 0.0.23 pyhcf101f3_0 conda-forge 19kB
+ fastapi-core 0.136.3 pyhcf101f3_0 conda-forge 96kB
+ fastar 0.11.0 py314h0b738fb_0 conda-forge 423kB
+ font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge Cached
+ font-ttf-inconsolata 3.000 h77eed37_0 conda-forge Cached
+ font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge Cached
+ font-ttf-ubuntu 0.83 h77eed37_3 conda-forge Cached
+ fontconfig 2.18.0 h27c8c51_0 conda-forge 281kB
+ fonts-conda-forge 1 hc364b38_1 conda-forge Cached
+ fonttools 4.63.0 pyh7db6752_0 conda-forge 846kB
+ freetype 2.14.3 ha770c72_0 conda-forge Cached
+ gflags 2.2.2 h5888daf_1005 conda-forge 120kB
+ glog 0.7.1 hbabe93e_0 conda-forge 143kB
+ h11 0.16.0 pyhcf101f3_1 conda-forge 39kB
+ h2 4.3.0 pyhcf101f3_0 conda-forge Cached
+ hpack 4.1.0 pyhd8ed1ab_0 conda-forge Cached
+ httpcore 1.0.9 pyh29332c3_0 conda-forge Cached
+ httptools 0.7.1 py314h5bd0f2a_1 conda-forge 99kB
+ httpx 0.28.1 pyhd8ed1ab_0 conda-forge Cached
+ hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge Cached
+ idna 3.17 pyhcf101f3_0 conda-forge 57kB
+ jinja2 3.1.6 pyhcf101f3_1 conda-forge Cached
+ kaleido-core 0.2.1 h3644ca4_0 conda-forge Cached
+ kiwisolver 1.5.0 py314h97ea11e_0 conda-forge 77kB
+ lcms2 2.19.1 h0c24ade_0 conda-forge 251kB
+ ld_impl_linux-64 2.45.1 default_hbd61a6d_102 conda-forge Cached
+ lerc 4.1.0 hdb68285_0 conda-forge Cached
+ libabseil 20260107.1 cxx17_h7b12aa8_0 conda-forge 1MB
+ libarrow 24.0.0 h6f10b76_3_cpu conda-forge 7MB
+ libarrow-acero 24.0.0 h635bf11_3_cpu conda-forge 592kB
+ libarrow-compute 24.0.0 h53684a4_3_cpu conda-forge 3MB
+ libarrow-dataset 24.0.0 h635bf11_3_cpu conda-forge 592kB
+ libarrow-substrait 24.0.0 hb4dd7c2_3_cpu conda-forge 502kB
+ libblas 3.11.0 8_h4a7cf45_openblas conda-forge 19kB
+ libbrotlicommon 1.2.0 hb03c661_1 conda-forge Cached
+ libbrotlidec 1.2.0 hb03c661_1 conda-forge Cached
+ libbrotlienc 1.2.0 hb03c661_1 conda-forge Cached
+ libcblas 3.11.0 8_h0358290_openblas conda-forge 19kB
+ libcrc32c 1.1.2 h9c3ff4c_0 conda-forge Cached
+ libdeflate 1.25 h17f619e_0 conda-forge Cached
+ libevent 2.1.12 hf998b51_1 conda-forge Cached
+ libexpat 2.8.1 hecca717_0 conda-forge 77kB
+ libffi 3.5.2 h3435931_0 conda-forge Cached
+ libfreetype 2.14.3 ha770c72_0 conda-forge Cached
+ libfreetype6 2.14.3 h73754d4_0 conda-forge Cached
+ libgfortran 15.2.0 h69a702a_19 conda-forge 28kB
+ libgfortran5 15.2.0 h68bc16d_19 conda-forge 2MB
+ libgoogle-cloud 3.5.0 h25dbb67_0 conda-forge 3MB
+ libgoogle-cloud-storage 3.5.0 hdbdcf42_0 conda-forge 780kB
+ libgrpc 1.78.1 h1d1128b_0 conda-forge 7MB
+ libjpeg-turbo 3.1.4.1 hb03c661_0 conda-forge Cached
+ liblapack 3.11.0 8_h47877c9_openblas conda-forge 19kB
+ libmpdec 4.0.0 hb03c661_1 conda-forge 92kB
+ libopenblas 0.3.33 pthreads_h94d23a6_0 conda-forge 6MB
+ libopentelemetry-cpp 1.26.0 h9692893_0 conda-forge 934kB
+ libopentelemetry-cpp-headers 1.26.0 ha770c72_0 conda-forge 396kB
+ libparquet 24.0.0 h7376487_3_cpu conda-forge 1MB
+ libpng 1.6.58 h421ea60_0 conda-forge 318kB
+ libprotobuf 6.33.5 h6eeba95_1 conda-forge 4MB
+ libre2-11 2025.11.05 h0dc7533_1 conda-forge 213kB
+ libsqlite 3.53.1 h0c1763c_0 conda-forge 955kB
+ libstdcxx-ng 15.2.0 hdf11a46_19 conda-forge 28kB
+ libthrift 0.22.0 h7d032f7_2 conda-forge 424kB
+ libtiff 4.7.1 h9d88235_1 conda-forge Cached
+ libutf8proc 2.11.3 hfe17d71_0 conda-forge 86kB
+ libuuid 2.42.1 h5347b49_0 conda-forge 40kB
+ libuv 1.52.1 h280c20c_0 conda-forge 420kB
+ libwebp-base 1.6.0 hd42ef1d_0 conda-forge Cached
+ libxcb 1.17.0 h8a09558_0 conda-forge Cached
+ markdown-it-py 4.2.0 pyhd8ed1ab_0 conda-forge 69kB
+ markupsafe 3.0.3 py314h67df5f8_1 conda-forge 27kB
+ mathjax 2.7.7 ha770c72_3 conda-forge Cached
+ matplotlib-base 3.10.9 py314h1194b4b_0 conda-forge 9MB
+ mdurl 0.1.2 pyhd8ed1ab_1 conda-forge Cached
+ munkres 1.0.7 py_1 bioconda Cached
+ narwhals 2.21.2 pyhcf101f3_0 conda-forge 284kB
+ nlohmann_json 3.12.0 h54a6638_1 conda-forge 136kB
+ nspr 4.38 h29cc59b_0 conda-forge Cached
+ nss 3.118 h445c969_0 conda-forge Cached
+ numpy 2.4.6 py314h2b28147_0 conda-forge 9MB
+ openjpeg 2.5.4 h55fea9a_0 conda-forge Cached
+ orc 2.3.0 h21090e2_0 conda-forge 1MB
+ packaging 26.2 pyhc364b38_0 conda-forge 92kB
+ pandas 3.0.3 py314hb4ffadd_0 conda-forge 15MB
+ perf_ssr 0.4.8 py_0 jitendralab 720kB
+ pillow 12.2.0 py314h8ec4b1a_0 conda-forge 1MB
+ pip 26.1.1 pyh145f28c_0 conda-forge 1MB
+ plotly 6.6.0 pyhd8ed1ab_0 conda-forge Cached
+ plotly-upset-hd 0.0.2 py_0 jitendralab 356kB
+ prometheus-cpp 1.3.0 ha5d0236_0 conda-forge 200kB
+ pthread-stubs 0.4 hb9d3cd8_1002 conda-forge Cached
+ pyarrow 24.0.0 py314hdafbbf9_0 conda-forge 27kB
+ pyarrow-core 24.0.0 py314h969be7f_0_cpu conda-forge 5MB
+ pydantic 2.13.4 pyhcf101f3_0 conda-forge 347kB
+ pydantic-core 2.46.4 py314h2e6c369_0 conda-forge 2MB
+ pydantic-extra-types 2.11.2 pyhcf101f3_0 conda-forge 74kB
+ pydantic-settings 2.14.1 pyhcf101f3_0 conda-forge 52kB
+ pygments 2.20.0 pyhd8ed1ab_0 conda-forge Cached
+ pyparsing 3.3.2 pyhcf101f3_0 conda-forge Cached
+ pysocks 1.7.1 pyha55dd90_7 conda-forge Cached
+ python 3.14.5 habeac84_100_cp314 conda-forge 37MB
+ python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge Cached
+ python-dotenv 1.2.2 pyhcf101f3_0 conda-forge Cached
+ python-kaleido 0.2.1 pyhd8ed1ab_0 conda-forge Cached
+ python-multipart 0.0.29 pyhcf101f3_0 conda-forge 38kB
+ python_abi 3.14 8_cp314 conda-forge 7kB
+ pyyaml 6.0.3 py314h67df5f8_1 conda-forge 202kB
+ qhull 2020.2 h434a139_5 conda-forge Cached
+ re2 2025.11.05 h5301d42_1 conda-forge 27kB
+ readline 8.3 h853b02a_0 conda-forge Cached
+ requests 2.34.2 pyhcf101f3_0 conda-forge 69kB
+ rich 15.0.0 pyhcf101f3_0 conda-forge Cached
+ rich-argparse 1.8.0 pyhd8ed1ab_0 conda-forge 27kB
+ rich-click 1.9.8 pyh8f84b5b_0 conda-forge 64kB
+ rich-toolkit 0.19.10 pyhcf101f3_0 conda-forge 33kB
+ s2n 1.7.3 hc5a330e_0 conda-forge 388kB
+ seqkit 2.13.0 he881be0_0 bioconda Cached
+ seqtk 1.5 h577a1d6_1 bioconda 142kB
+ shellingham 1.5.4 pyhd8ed1ab_2 conda-forge Cached
+ six 1.17.0 pyhe01879c_1 conda-forge Cached
+ snappy 1.2.2 h03e3b7b_1 conda-forge Cached
+ sniffio 1.3.1 pyhd8ed1ab_2 conda-forge Cached
+ sqlite 3.53.1 hbc0de68_0 conda-forge 205kB
+ starlette 1.1.0 pyhcf101f3_0 conda-forge 64kB
+ tk 8.6.13 noxft_h366c992_103 conda-forge Cached
+ tomli 2.4.1 pyhcf101f3_0 conda-forge 22kB
+ tqdm 4.67.3 pyh8f84b5b_0 conda-forge Cached
+ typer 0.26.3 pyhcf101f3_0 conda-forge 184kB
+ typing-extensions 4.15.0 h396c80c_0 conda-forge Cached
+ typing-inspection 0.4.2 pyhcf101f3_2 conda-forge 21kB
+ typing_extensions 4.15.0 pyhcf101f3_0 conda-forge Cached
+ tzdata 2025c hc9c84f9_1 conda-forge Cached
+ unicodedata2 17.0.1 py314h5bd0f2a_0 conda-forge 410kB
+ upsetplot 0.9.0 pyhd8ed1ab_1 conda-forge 28kB
+ urllib3 2.7.0 pyhd8ed1ab_0 conda-forge 104kB
+ uvicorn 0.48.0 pyhc90fa1f_0 conda-forge 56kB
+ uvicorn-standard 0.48.0 he364bde_0 conda-forge 4kB
+ uvloop 0.22.1 py314h5bd0f2a_1 conda-forge 593kB
+ watchfiles 1.2.0 py314ha5689aa_0 conda-forge 416kB
+ websockets 16.0 py314h0f05182_1 conda-forge 383kB
+ xorg-libxau 1.0.12 hb03c661_1 conda-forge Cached
+ xorg-libxdmcp 1.1.5 hb03c661_1 conda-forge Cached
+ yaml 0.2.5 h280c20c_3 conda-forge Cached
+ zlib 1.3.2 h25fd6f3_2 conda-forge Cached
+ zlib-ng 2.3.3 hceb46e0_1 conda-forge Cached

Summary:

Install: 186 packages

Total download: 142MB

─────────────────────────────────────────────────────────────────────────────────────────────────

Transaction starting
libgrpc 7.0MB @ 2.3MB/s 3.0s
numpy 8.9MB @ 2.3MB/s 3.8s
matplotlib-base 8.5MB @ 2.0MB/s 4.2s
libarrow 6.5MB @ 2.3MB/s 2.8s
pandas 15.3MB @ 2.5MB/s 6.2s
libopenblas 5.9MB @ 2.3MB/s 2.5s
pyarrow-core 4.8MB @ 1.6MB/s 3.0s
libprotobuf 3.7MB @ 2.4MB/s 1.6s
aws-sdk-cpp 3.6MB @ 3.1MB/s 1.2s
biopython 3.4MB @ 2.0MB/s 1.7s
libgfortran5 2.5MB @ 2.6MB/s 1.0s
libgoogle-cloud 2.6MB @ 2.4MB/s 1.1s
pydantic-core 1.9MB @ 2.7MB/s 0.7s
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Transaction finished

(jitENV) hp@hp-HP-Z2-Tower-G9-Workstation-Desktop-PC:~/jitendraTEST$ crossroad -h

Usage: crossroad [OPTIONS]

Run the main croSSRoad analysis pipeline, or manage jobs.

╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --version -v Show version, logo, citation, and links. │
│ --install-completion Install completion for the current shell. │
│ --show-completion Show completion for the current shell, to copy it or customize the installation. │
│ --help -h Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Mode Selection ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --api -a Run the Crossroad web API server. │
│ --slurm -s Submit the analysis job to a Slurm cluster. │
│ --job-status JOB_ID Query the status of a specific job ID. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Input Files (provide --input-dir OR --fasta) ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --input-dir -i PATH Directory containing: `all_genome.fa`, ``, ``. Exclusive with `--fasta`. │
│ --fasta -fa PATH Input FASTA file (e.g., `all_genome.fa`). Alternative to `--input-dir`. │
│ --categories -c PATH Genome categories TSV file. Optional if using `--fasta`. Ignored if `--input-dir` is used (looks for `genome_categories.tsv` inside). │
│ --gene-bed -b PATH Gene BED file for SSR-gene analysis. Optional. If `--input-dir` is used, looks for `gene.bed` inside. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Analysis Parameters ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --reference-id -ref TEXT Reference genome ID for comparative analysis. Optional parameter for reference-based comparisons. │
│ --output-dir -o DIRECTORY Base output directory for jobs. Overrides CROSSROAD_JOB_DIR env var. │
│ --flanks -f Process flanking regions. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ PERF SSR Detection Parameters ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --mono INTEGER Mononucleotide repeat threshold. [default: 12] │
│ --di INTEGER Dinucleotide repeat threshold. [default: 6] │
│ --tri INTEGER Trinucleotide repeat threshold. [default: 4] │
│ --tetra INTEGER Tetranucleotide repeat threshold. [default: 3] │
│ --penta INTEGER Pentanucleotide repeat threshold. [default: 3] │
│ --hexa INTEGER Hexanucleotide repeat threshold. [default: 2] │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Filtering Parameters ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --min-len -l INTEGER Minimum genome length for filtering. [default: 1000] │
│ --max-len -L INTEGER Maximum genome length for filtering. [default: 10000000] │
│ --unfair -u INTEGER Maximum number of N's allowed per genome for Crossroad analysis. [default: 0] │
│ --repeat-threshold -rc INTEGER Repeat count Threshold for hotspot filtering (keeps records > this value). [default: 1] │
│ --genome-threshold -g INTEGER Genome count Threshold for hotspot filtering (keeps records > this value). [default: 2] │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Performance & Output ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --threads -t INTEGER Number of threads for Crossroad analysis. [default: 50] │
│ --plots -p Enable plot generation. │
│ --intrim-dir TEXT Name for the intermediate files directory (within the main job output dir). [default: intrim] │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

(jitENV) hp@hp-HP-Z2-Tower-G9-Workstation-Desktop-PC:~/jitendraTEST$

mrFAST: Micro Read Fast Alignment Search Tool

Neel — Tue, 26 Apr 2016 03:50:06 -0500

mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes how to choose the parameters and tune mrFAST with respect to the library settings. mrFAST is designed to find 'all' mappings for a given set of reads, however it can return one "best" map location if the relevant parameter is invoked.

More at http://mrfast.sourceforge.net/manual.html

Address of the bookmark: http://mrfast.sourceforge.net/manual.html

mafTools

Radha Agarkar — Sat, 21 May 2016 22:40:21 -0500

Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.

Address of the bookmark: https://github.com/dentearl/mafTools

SpeedSeq

Jit — Fri, 20 Jan 2017 06:05:43 -0600

A flexible framework for rapid genome analysis and interpretation

C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth (2015). doi:10.1038/nmeth.3505.

http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html

Address of the bookmark: https://github.com/hall-lab/speedseq

sockeye

Jit — Fri, 17 Feb 2017 08:51:16 -0600

This sockeye software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization.

Address of the bookmark: http://www.bcgsc.ca/platform/bioinfo/software/sockeye/releases/1.3

bedtools

Jit — Fri, 24 Feb 2017 04:50:44 -0600

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one tointersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

bedtools is developed in the Quinlan laboratory at the University of Utah and benefits from fantastic contributions made by scientists worldwide.

Address of the bookmark: http://bedtools.readthedocs.io/en/latest/index.html

Salzberg lab

Mon, 15 May 2017 05:14:01 -0500

We are a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with biomedical scientists to apply these methods to current problems arising in a broad spectrum of biological and medical research areas. We’re also part of the Center for Computational Biology, a group of 20+ faculty members and their labs at Johns Hopkins working on computational, statistical, and mathematical methods that can turn massive genomic data sets into biologically and clinically useful information.

https://salzberg-lab.org/

Awesome perl frameworks, libraries and software - PART 3

Neel — Fri, 07 Jul 2017 04:10:32 -0500

fujiwara/perl-queue-q4pg-lite - simple message queue using PostgreSQL.
formbuilder/formbuilder - Perl CGI::FormBuilder module for generating, validating, and processing HTML forms
fastly/fastly-perl - Fastly perl client
ewilded/SCARY - PHP Source Code Analyzer written in Perl (taint checking)
esobchenko/rest-google - REST::Google provides OO access to Google REST API from Perl
Ensembl/Bio-DB-HTS - Git repo for Bio::DB::HTS module on CPAN, providing Perl links into HTSlib
eblah/E-Blah-Forum - E-Blah is a Perl-based forum system started in 2001.
dominikschulz/Zabbix-Sender - A pure-perl implementation of zabbix-sender.
derf/Travel-Status-DE-IRIS - IRIS Perl API (German and partially european railway departure monitor)
Debian/devscripts - Mirror of https://anonscm.debian.org/cgit/collab-maint/devscripts.git
ddmitov/camel-doctor - Desktop HTML User Interface for the default Perl 5 Debugger
dan-blanchard/io-storm - Perl support for Apache Storm distributed computation system.
dajobe/logger - Perl IRC logger
dagolden/Hash-Ordered - A compact, pure-Perl ordered hash class
dagolden/getopt-lucid - (Perl) Clear, readable syntax for command line processing
craigslist/perl-AnyEvent-Redis-Federated - An event-based redis client that implements client-side sharding in Perl.
cosimo/perl5-device-modem - Device::Modem CPAN module, interface to any AT-command-set based device
CindyLinz/Perl-AnyEvent-MySQL - Pure Perl AnyEvent socket implementation of MySQL client
chorny/test-warn - Perl extension to test methods for warnings
cho45/List-Enumerator - List::Enumerator is like ruby's Enumerator. (Perl)
bingos/module-install-readmefrompod - (perl) A Module::Install extension to automatically convert POD to a README
bingos/bot-gumbynet - (perl) The GumbyNET bot code
aufflick/p5-net-apns-persistent - Persistent Apple APNS interface for Perl 5
ddmitov/perl-executing-browser - HTML User Interface for Perl 5 Desktop Applications
phatblat/app-store-rank - A simple Perl script which scrapes the 62 app stores worldwide for the current app ranking
Easy-Forex/Verify-emails - Quick perl script to check a list of email addresses for valid and bogus.
warewolf/Procmon - A perl command toolkit for analysis of XML procmon logs
typester/data-amf - perl module for serialize/deserialize adobe's AMF data
thibaultduponchelle/tryperl - Try Perl: learn the basics of the Perl language in your browser
syohex/new-tohoho - Modernize 「とほほの perl入門」
simcop2387/perlbuut - new version of perlbot, based on buubot
rjray/image-size - A Perl module to read the dimensions of images in several popular formats
perigrin/flexo-bot - A Rewrite of the Bender IRC bot from irc.perl.org using the Adam/Moses framework
norm/p5-Media - Perl modules and scripts for handling the conversion and storage of media
nkakuev/list-cpp-warning-options - A simple Perl script that prints GCC warning options you can apply to C++ code.
mscoutermarsh/RRD-to-CSV - Perl script to convert RRD data to CSV
mones/clawsker - This is a clone from main repository at http://git.claws-mail.org: Clawsker is a Perl-GTK2 applet to edit hidden preferences for Claws Mail, and to do it in a safe and user friendly way, preventing users from raw editing of configuration files.
mackers/passook - Passook is a perl script that automatically generates passwords. Passook is customizable so that you can choose different levels between a very pronounceable or a very secure password. Passook can be run in a unix shell or as a cgi script.
lecstor/PDF--Boxer - Perl module to create PDF documents from "simple" templates.
jmcnamara/app-pod2epub - A Perl Module for converting Pod to ePub eBooks.
jjn1056/Example-PlackStreamingAndNonblocking - Examples of Perl Plack / PSGI streaming and nonblocking
hoytech/Valence-p5 - Perl interface to valence/electron GUI toolkit
erinspice/geni-automerge - A tool written in Perl using the Geni.com API which automatically merges sufficiently similar profiles.
eilara/camel-defense - A very simple tower defense game in Perl
clintongormley/ElasticSearchX-Autocomplete - ElasticSearchX::Autocomplete is a Perl module which gives you frequency (and optionally geolocation)-sensitive autocomplete suggestions based on your data
audreyt/encode-hanconvert - [Perl] Modules and scripts for Traditional and Simplified Chinese mappings
szabgab/perltv.org - The source code of the Perl TV
rhandom/perl-net-server - Perl Module Net::Server
plotly/Perl-API - Perl-API for beautiful, interactive, & shareable graphs
MerijntjeTak/vyattaLookingGlass - Looking glass for the Vyatta routing suite
KES777/Devel-DebugHooks - Perl debugger
jonasbn/perl-workflow - Simple, flexible system to implement workflows
inway/mojo-rabbitmq-client - Mojo::IOLoop based RabbitMQ (AMQP) client
ingydotnet/yaml-pm - YAML Perl Module
gtsafas/mailgun.perl - Perl wrapper for mailgun
abaez/perl - Learning Perl
technix/Perl-Analyzer - Perl source analyzer - view namespaces, dependencies, inheritance and much more
zigorou/perl-json-patch - A Perl implementation of JSON Patch
Yaribz/SPADS - SpringRTS Perl Autohost for Dedicated Server
vti/app-prf - Perl refactoring tool
TvdW/perl-DBD-Cassandra - DBD::Cassandra is a DBI driver for Cassandra/CQL3
topaz/perl-mandelbrot - Interactive Mandelbrot set renderer/explorer for your terminal.
tociyuki/libtext-ampita-perl - Template generator from a xhtml document and runtime for it.
tene/perl6-sqlite - SQLite3 for Perl 6
smarx/waz-storage-perl - Small library for working with Windows Azure storage from Perl
scottchiefbaker/perl-git-prompt - Git extension for the bash prompt
sbober/levitation-perl - perl port of scy's levitation
salva/p5-Net-SFTP-Foreign - Perl SFTP client
russoz/perltests - Small scripts to test constructs - mostly for myself.
robrwo/Perl-Rewrite - Munge Perl Code
rjbs/IPC-Run3 - (Perl) run a subprocess with input/ouput redirection
rjbs/Email-Simple - the Email-Simple perl distribution
ritou/p5-oidc-lite - OIDC::Lite - Perl Library of OpenID Connect
pjf/WebService-HabitRPG - Access the HabitRPG API from Perl
pjf/trillr - Perl tip example code
PerlBone/PerlBone - PerlBone allows you to write Arduino Style software in Perl for the BeagleBone. It is to Perl what BoneScript is to Javascript
Ovid/code-cutnpaste - Find cut-n-pasted Perl code
mfontani/Net-Amazon-Route53 - Perl interface to Amazon's Route 53 service
maxmind/GeoIP2-perl - Perl API for MaxMind's GeoIP2 web services and databases
maros/CatalystX-I18N - Perl I18N Toolkit for the Catalyst MVC
marcusramberg/text-simpletable - The Text::SimpleTable perl distribution
lovelle/perl-disque - Perl client for Disque, an in-memory, distributed job queue
leto/math--matrixreal - Matrices of real numbers in Perl
Klortho/Physics-Unit - Perl Physics::Unit module
kentaro/perl-project-libs - Include modules libs automatically
karpet/search-query-perl - Search::Query - polyglot query parsing
jplindstrom/p5-Devel-PerlySense - CPAN module Devel::PerlySense
hvoers/PNL - Site for Perl mongers in NL
HouzuoGuo/PerlDB - This is a programming exercise, do not use in serious code.
hirose31/p5-InfluxDB - Perl client library for InfluxDB
grantm/XML-SAX - Simple API for XML including pure Perl parser
GeneticGenesis/Perl-Ferment - Yet another tool to manage perl installs in your home directory.
Ensembl/ensembl-funcgen - Ensembl Funcgen Perl API and SQL schema
dk/Win32-GuiTest - Perl GUI Test Utilities
depesz/Pg--Explain - Pg::Explain Perl module
dann/p5-perl-metrics-lite - Pluggable Perl Metrics System
daisieh/phylogenomics - (Mostly) Perl scripts that do something related to phylogenomic analysis.
carwynmoore/perl-nats - A Perl client for the NATS messaging system
briandfoy/test-prereq - (Perl) check if Makefile.PL has the right pre-requisites
briandfoy/cpan-packagedetails - (Perl) This is what the module does
bingos/cpanplus-yacsmoke - (perl) Yet Another CPANPLUS Smoke Tester
beanz/net-mqtt-perl - Perl implementation of MQTT Protocol (http://mqtt.org)
perl6/book - Using Perl 6 - an unfinished book about Perl 6
lukec/stripe-perl - Perl library to connect to the Stripe API
c0bra/image-wordcloud-perl - Perl module for generating pretty wordcloud images
bradfitz/set-consistenthash-perl - consistent hashing library for Perl
wolfman2000/Perl-6-Pastebin - A pastebin written in Perl 5 to host content specifically meant for Perl 6.
njh/perl-net-rtp - Perl Module : Send and receive RTP packets (RFC3550)
beanz/net-pachube-perl - Perl Interface to Pachube
apparentlymart/perl-anyevent-websocket - WebSocket implementation for AnyEvent
tsee/ZMQ-Declare-Perl - The ZMQ::Declare Perl module for declarative use of 0MQ
sjohnston/Net-Zabbix - Perl wrapper for Zabbix API
reneeb/Perl-Critic-OTRS - A collection of Perl::Critic policies to program in the OTRS way.
masak/csv - A parser for CSV (comma-separated values) files for Perl 6
jtbraun/Parse-RecDescent - Perl module for generating recursive-descent parsers
jjn1056/perl-recruiting-web - webpages for helping recruiters and perl programmers understand each other better
chef-boneyard/chef-install - A perl based installer for Chef
pvande/Template-Mustache - Drawing Mustaches on Perl, for fun and profit
schwern/Paths - Grand Unified Perl File and Directory Objects
schwern/Gravatar-URL - Perl module to make URLs for Gravatars from an email address
p5-shorten/WWW-Shorten-Yourls - Perl module for shortening URLs using yourls.org
juliensobrier/Net-Google-SafeBrowsing2 - Google Safe Browsing v2 library for Perl
EntropyOrg/p5-Devel-IPerl - Perl language kernel for Jupyter http://jupyter.org/
PerlChina/HeadFirstMoose - 使用Perl + Moose实现《Head First Design Pattern》的大部分例子
mudler/GitInsight - Predict your github contributions using Bayesian inference and Markov chain with perl and PDL
dagolden/File-chdir - (Perl) a more sensible way to change directories
potyl/perl-App-deckjs2pdf - Convert a Deck.JS presentation to PDF
Perl-Toolchain-Gang/Sub-Uplevel - (Perl) apparently run a function in a higher stack frame
mlawren/p5-OptArgs - Integrated option and argument processing for Perl scripts
masterzen/redis-snmp - A perl net-snmp agentX to export Redis performance counters
masochist/modern-perl-cpan-task-kensho - The repository for the upcoming book, Modern Perl with CPAN
jeffa/DesignPatterns-Perl - Perl (with Moose) implementations of the Gang of Four Design Patterns
agentzh/makefile-parser-pm - Perl CPAN module Makefile::Parser - A simple parser for Makefiles
Real-Gecko/filemin - File manager for Webmin written completely in perl
andreas-marschke/nagios-nrpe - A pure perl implementation of the Nagios NRPE daemon and client
syohex/zsh-perl-completions - zsh completions for Perl utilties
pclinger/SonyCameraRemote - Sony Camera Remote API - Perl Implementation
patch/cldr-number-pm5 - CLDR::Number (Perl 5): Localized number formatters using the Unicode CLDR
ollyg/Net-CLI-Interact - Development of Net::CLI::Interact Perl distribution
nothingmuch/continuation-delimited - delimited continuations for Perl 5
nmelnick/whatbot - whatbot: A sane bot for most chat applications, written in modern Perl
naoya/list-rubylike - Ruby-like list operations for perl
miyagawa/CPAN-Any - Install Perl modules using any CPAN clients
miki/Algorithm-LSH - perl implementation of Locality Sensitive Hashing
kimmel/basic-perl-template-for-cli - A basic template for Perl applications that take and parse command line options. Based on the ideas from Perl Best Practices and the GNU style long options reference. It uses only Standard Modules to maintain portability.
gardejo/moose-presentations - Perl Moose course in Japanese
dpavlin/Biblio-RFID - perl tools to use different RFID readers for library use
chef/chef-install - A perl based installer for Chef
bingos/smokebrew - (perl) Automated Perl building and installation for CPAN Testers
andrewrjones/perl5-App-MP4Meta - Apply iTunes-like meta data to an mp4 file
admc/irssi-growlnotify - Creating Growl notifications from various Irssi events, using growlnotify and Irssi Perl.
plack/psgi-specs - PSGI (Perl WSGI) specifications
libwww-perl/uri - The Perl URI:: module
autarch/DateTime.pm - A date and time object for Perl
zostay/P6SGI - Proposed Standard for Perl 6 Web Server Gateway Interface Specification
cooper/yiria - the current generation of juno-ircd, an IRC server daemon written in the Perl programming language. it's very modular and event-driven, designed specifically to be extensible and aims to implement all modern features of IRC, including those of many recently-defined specifications.
wertarbyte/hetzner-rdns - update reverse DNS settings for systems hosted at Hetzner; a successor (hetzner-robot-perl) is in preparation to utilise the webservice interface
spencertipping/canard - A functional concatenative language implemented in Linux/AMD64 machine code and self-modifying perl
sni/Monitoring-Generator-TestConfig - Perl extension for generating test monitoring configurations (nagios/icinga/shinken)
slazar/Panasonic-LF20-control - Perl Scripts to control the Panasonic LF20 LCD TV Series
sabujp/nfsSpeedTest - nfsSpeedTest is a wrapper for dd written in Perl. It was created mainly for testing the performance of file systems or network file shares (e.g. NFS), but can be used for generating large files (e.g. swap files) or for testing the network
quietfanatic/link-c - Easily use C libraries in Rakudo Perl 6
pjain/WWW-Shorten-Yourls - Perl module for shortening URLs using yourls.org
nightsailer/net-sinaweibo - A lightweight Perl OAuth api for SinaWeibo(新浪微博)
mbethke/Ashafix - A Postfixadmin clone in Perl/Mojolicious
kzys/test-mock-recorder - Record-and-verify style mocking library for Perl
kpumuk/mysqlsla-bdb - MySQL Slow Logs Analyzer optimized to work with huge logs (use BerkeleyDB instead of perl hashes)
hernan604/Web-IRC - The purpose of Web::IRC is to help team communication. Web::IRC uses channel concept from IRC. Slack.com clone in perl <3
duckduckgo/p5-duckpan-installer - DuckPAN Perl Installer
dnmfarrell/Perly-Bot - a RSS trawler and social media broadcaster
PDLPorters/PDL-Stats - Statistics modules in Perl Data Language, with a quick-start guide for non-PDL people. They make the PDL shell work like R, but with PDL threading (fast automatic iteration) of procedures including t-test, linear regression, and k-means clustering.
CPAN-API/metacpan-client - Home of the official MetaCPAN Perl API client.
rrb3942/perl-Asterisk-AMI - A Perl module for interfacing with the Asterisk Management Interface.
rafl/perlfaq - History of the perlfaq distribution before it got moved to https://github.com/tpf/perlfaq
mithun/perl-tmdb - TMDB - Perl wrapper for The MovieDB API
hyphaltip/htbda_perl_class - High Throughput Biological Data Analysis using Perl
gmcharlt/marc-perl - MARC/Perl (mirror of git://git.code.sf.net/p/marcpm/code)
cosimo/perl5-http-dav - Perl5 HTTP::DAV CPAN module, interface to WebDAV-enabled HTTP servers
copperly/Perl-Tutorial - Tutorial for Perl
apocalypse/perl-dist-zilla-plugin-authority - add an $AUTHORITY to your packages
DrHyde/perlscripts - Random scripts
perl6/DBIish - Database interface for Perl 6
shlomif/mastering-perl - A copy of brian d foy's mastering-perl book.
Prajithp/letsencrypt-cpanel - cPanel/WHM plugin for Let's Encrypt client (uses perl and WHM API)
mikecardwell/pipe2imap - Pipe2IMAP is a Perl script that will take IMAP options from the command line arguments, and an email from a PIPE, and will deliver the message via IMAP
silverstripe-labs/silverstripe-unidecode - Unidecode is a PHP version of the perl module Text::Unicode. It takes UTF-8 data and tries to represent it in US-ASCII characters.
exhuma/jsttyplay - A set of scripts written in Perl and JavaScript to allow ttyrec logs to be played back in a web browser.
demianriccardi/HackaMol - Object-Oriented Perl 5, Moose Library for Molecular Hacking
davorg/www-shorten - Perl interface to various URL-shortening sites
agentzh/queue-memcached-buffered - Perl client library for memcacheq operations
toronto-perl-mongers/tpm-website - Toronto Perl Mongers Website
odyniec/p5-WebService-Amazon-Route53 - Perl interface to Amazon Route 53 API
neilb/perl-hub - Proof of concept for "front page for the perl community"
mschilli/proc-simple-perl - Proc::Simple CPAN Module
makamaka/geohex-perl - geohex perl implementation (Geo::Hex)
gslin/thrift-perl - Perl module of Thrift
djzort/Net-DHCP - Perl module Net::DHCP
cosimo/perl5-test-device-serialport - A mock object to test virtual serial port-based devices
afair/resque-perl - Resque ported to perl
PerlChina/Newbie-Gift - A tool suite for perl newbie.
Perl-Email-Project/Email-Send - perl library for sending email
Lemonade-Stand/Lemonade - Perl E-commerce Solution
atomicules/TTYtter - Unofficial maintenance and mirror of Floodgap's TTYtter: an interactive console text-based command-line Twitter client and Perl platform (whew!)
worldmind/perl-test-code-quality-template - Some tests for non-functional testing - you can copy these test to any your perl project
dpavlin/perl-fuse - write filesystems in Perl using FUSE
rjbs/Email-Valid - perl library to validate email addresses
masak/gge - Glacial Grammar Engine -- a Perl 6 grammar engine written in Perl 6
masak/druid - A connection-oriented board game written in Perl 6
harisekhon/lib - Perl & Python Utility Library for my other repos
tempire/riak-tiny - Perl interface to Riak without Moose
oz/tiny_wiki - 50 lines of Perl to play around with Dancer and KiokuDB
goozbach/perl-Net-Disqus - A Perl library for the Disqus API -- Deprecated
borisdaeppen/VM-JiffyBox - Perl API for JiffyBox
apeiron/modern-perl-cpan-task-kensho - The repository for the upcoming book, Modern Perl with CPAN
ajolma/geoinformatica - Geoinformatica is a geospatial toolkit that builds on GDAL, Perl and GTK+
Weborama/Riak-Light - Fast and lightweight Perl client for Riak
zostay/owasp-esapi-perl - OWASP Enterprise Security API for Perl
yannk/perl-net-appnotifications - perl5 interface to www.appnotifications.com: easily deliver push notifications to your iPhone
three18ti/Reddit.pm - Perl wrapper for the reddit API
sukria/Test-TinyMocker - Minimal yet very useful mocker for Perl
solgenomics/yapri - Yet Another Perl R Inteface.
rclasen/workout - Workout file perl library
pshangov/perldoc-vim - Perldoc viewer for vim with syntax highlighting
olof/transmission-client - Perl interface to Transmission bittorrent client
ogawa/cybozu2ical-perl - Converting Cybozu Office Scheduler data to iCalendar format.
motemen/perl5-Print-Indented - Outputs indented as per source code indentation
miknight/pisg - Perl IRC Statistics Generator
melo/bash-completion - A Perl distribution to create your own bash completion solutions
mantovani/SPPM-Web - São Paulo Perl Mongers website.
jzawodn/perl-Algorithm-TopPercent - A perl module for tracking the top-N most frequent items in a streaming data set using fixed memory.
jmlynesjr/wxPerl-Module-Examples - wxPerl-Module-Examples not from the wxBook
doy/parse-keyword - DEPRECATED: write syntax extensions in perl
chromatic/Test-MockObject - The Test::MockObject Perl 5 library from the CPAN
chrisa/perl-Net-ZooKeeper - Net::ZooKeeper Perl module
apparentlymart/activity-streams-perl - Activity Streams Library for Perl
andrewalker/p5-webservice-digitalocean - Perl module for DigitalOcean's RESTful API
Starlink/perl-Astro-FITS-HdrTrans - Perl module for performing astronomical metadata header translations from FITS to generic and back.
Rio-Perl-Mongers/rio.pm.org - Site da Rio Perl Mongers
sitaramc/gitolite - Hosting git repositories -- Gitolite allows you to setup git hosting on a central server, with very fine-grained access control and many (many!) more powerful features. [IMPORTANT: please click and read the WIKI link above before submitting issues, pull requests, etc] IMPORTANT: PLEASE READ Nov 2 2014 UPDATE ABOUT DONATIONS -- see wiki
openresty/lua-nginx-module - Embed the Power of Lua into NGINX
sarabander/sicp-pdf - SICP PDF with Texinfo and LaTeX source
openresty/ngx_openresty - Turning Nginx into a Full-fledged Web App Server
petdance/ack - This repository is for ack 1.x, which is no longer being maintained. DO NOT SUBMIT ISSUES HERE. ack 2.0 has a new GitHub project at
openresty/nginx-tutorials - Nginx Tutorials
creaktive/rainbarf - CPU/RAM/battery stats chart bar for tmux (and GNU screen)
thoughtbot/rcm - rc file (dotfile) management
prey/prey-bash-client - Bash client for the Prey anti-theft software (Mac, Windows, Linux). The original.
lulzlabs/AirChat - Free Communications For Everyone.
k4rthik/git-cal - github like contributions calendar on terminal
munin-monitoring/contrib - Contributed stuff for munin (plugins, tools, etc...)
duckduckgo/duckduckgo - DuckDuckGo Instant Answer Infrastructure
nbs-system/naxsi - NAXSI is an open-source, high performance, low rules maintenance WAF for NGINX
DHowett/theos - Unified cross-platform iPhone Makefile system
git-deploy/git-deploy - Tool to manage using git as a deployment management tool
munin-monitoring/munin - Main repository for munin master / node / plugins
theory/sqitch - Sane database change management
jonreid/XcodeCoverage - Code coverage for Xcode projects
dalibo/pgbadger - a fast PostgreSQL Log Analyzer
nferraz/st - simple statistics from the command line
yuki-kimoto/gitprep - Github clone. you can install Github system into your unix/linux machine.
miyagawa/cpanminus - cpanminus - get, unpack, build and install modules from CPAN
sullo/nikto - Nikto web server scanner
sontek/dotfiles - My configuration files (.screenrc, .vimrc, .weechat, .bashrc, .gitconfig, etc)
PenturaLabs/Linux_Exploit_Suggester - Linux Exploit Suggester; based on operating system release number
RexOps/Rex - A framework for server orchestration and to simplify system administration
hokaccha/nodebrew - Node.js version manager
pasky/speedread - A simple terminal-based open source Spritz-alike (per-word RSVP aligned on optimal reading points)
plack/Plack - PSGI toolkit and server adapters
get-iplayer/get_iplayer - A utility for downloading TV and radio from BBC iPlayer
jfhovinne/jFeed - jQuery RSS/ATOM feed parser plugin
openresty/lua-resty-redis - Lua redis client driver for the ngx_lua based on the cosocket API
StefanSchroeder/Golang-Regex-Tutorial - Golang - Regular Expression Tutorial
openresty/nginx-systemtap-toolkit - Real-time analyzing and diagnosing tools for Nginx based on SystemTap
webfrogs/xcode_shell - shell script that used to auto-build xcode project
linode/cli - Command-line interface to the Linode platform
agentzh/code2ebook - Generate ebooks in various formats from source trees in various programming languages
timkay/aws - Easy command line access to Amazon EC2, S3, SQS, ELB, and SDB (new!)
webmin/webmin - Webmin source code
freebsdgirl/ggautoblocker - Good Game Auto Blocker
openresty/headers-more-nginx-module - Set, add, and clear arbitrary output headers
swcarpentry/bc - This repository is now frozen - please see the note below.
sm/sm - S{cripting,ystem,tack} Management (SM) Framework (Core)
alestic/ec2-consistent-snapshot - Initiate consistent EBS snapshots in Amazon EC2
bestpractical/rt - Request Tracker, an enterprise-grade issue tracking system
trapd00r/ls-- - ls on steroids
movabletype/movabletype - Movable Type
gotgit/gotgit - Errata and resources for GotGit: a book about Git in Chinese
ljunkie/plexWatch - Notify and Log watched content on a Plex Media Server
joeyh/myrepos - Multiple Repository management tool
xypiie/spread0r - spread0r is a txt reader, which makes your reading twice as fast as usual
linode/longview - Linode Longview Agent
philovivero/distribution - Short, simple, direct scripts for creating ASCII graphical histograms in the terminal.
mysociety/fixmystreet - This is mySociety's popular map-based reporting platform: easy to install in new countries and regions
spencertipping/js-in-ten-minutes - JavaScript in Ten (arbitrarily long) Minutes
kazeburo/GrowthForecast - Lightning Fast Graphing/Visualization
qooob/authentic-theme - Webmin/Usermin/Virtualmin/Cloudmin theme based on Bootstrap and Font Awesome
jbittel/httpry - HTTP logging and information retrieval tool
zakk4223/CocoaSplit - Stream/record your desktop/webcam to twitch/owned etc.
miyagawa/github-growler - Growl github updates
VividCortex/johnny-deps - Barebones dependency manager for Go.
dotphiles/dotphiles - A community driven framework of dotfiles.
CPAN-API/metacpan-web - Web interface for MetaCPAN
worlduniting/bookshop - bookShop is a publishing framework for html-to-pdf/(e)book toolchain happiness and sustainable productivity.
duncs/clusterssh - Cluster SSH - Cluster Admin Via SSH
leedo/noembed - oEmbed gateway service with additional non-oEmbed sources
cxreg/smartcd - Alter your bash (or zsh) environment as you cd
perl-catalyst/catalyst-runtime - The Elegant MVC Web Application Framework
Flipkart/HostDB - HostDB: a new tool to help manage data center inventory and write applications around it.
metabrainz/musicbrainz-server - The official musicbrainz-server codebase
monsieurvideo/get-flash-videos - Download or play videos from various Flash-based video hosting sites, without having to use the Flash player.
c9s/Vimana - Vimana is an easy to use system for searching , installing, and downloading vim script. Vimana provides a command-line interface such like aptitude programe on Debian linux, for you to search , download , install , upgrade scripts from http://www.vim.org (vimonline site).
Logitech/slimserver - Server for Logitech Squeezebox players. This server is also called Logitech Media Server
weijianwen/SJTUThesis - XeLaTeX templates for Shanghai Jiao Tong University (SJTU) thesis
hadley/ggplot2-book - The ggplot2 book
irssi/scripts.irssi.org - Script Repository for Irssi
bucardo/check_postgres - Nagios check_postgres plugin for checking status of PostgreSQL databases
harisekhon/nagios-plugins - Advanced Nagios Plugins - Hadoop, NoSQL datastores. Extends Nagios monitoring capabilities significantly further in to the application layer including Hadoop, Big Data, NoSQL and Web Scale technologies, APIs etc.
benbernard/RecordStream - commandline tools for slicing and dicing JSON records.
iberianpig/xSwipe - Multitouch gestures on X11, Linux
jimeh/manservant - Browse man pages in style with your personal manservant.
joeyh/ikiwiki - a wiki compiler
Zentyal/zentyal - Linux Small Business Server
yaoweibin/nginx_ajp_module - support AJP protocol proxy with Nginx
CPAN-API/cpan-api - A free, open API for everything you want to know about CPAN
neldredge/mathgen - See http://thatsmathematics.com/mathgen/
jtaby/Waldo - A generic port of TextMate's Find-In-Project, with associated MacVim plugin
broquaint/Gitalist - A modern git web viewer
rtomayko/shocco - shocco is a quick-and-dirty, literate-programming-style documentation generator for / in POSIX shell
pjf/exobrain - Automate your life with Exobrain
miyagawa/plagger - Pluggable RSS/Atom aggregator
justone/dotfiles - Dotfiles
jsierles/chef_cookbooks_deprecated - Opinionated chef recipes for Ubuntu/Debian. Manage nginx, unicorn, UNIX user accounts, postgresql, and more!
mattiasgeniar/varnish-4.0-configuration-templates - Configuration templates used for Varnish 4.0 implementations.
openresty/lua-resty-mysql - Nonblocking Lua MySQL driver library for ngx_lua
proger/eflame - Flame Graph profiler for Erlang
openresty/stapxx - Simple macro language extentions to systemtap
dkogan/feedgnuplot - Tool to plot realtime and stored data from the commandline, using gnuplot. This is the repo for 'feedgnuplot' on CPAN
wbraswell/rperl - RPerl Compiler
petdance/bobby-tables - bobby-tables.com, the site for preventing SQL injections
pshved/timeout - A script to measure and limit CPU time and memory consumption of black-box processes in Linux
openresty/srcache-nginx-module - Transparent subrequest-based caching layout for arbitrary nginx locations.
dockerana/dockerana - Docker Monitoring with support for Grafana and Graphite
OTRS/otrs - The OTRS framework.
bucardo/bucardo - Bucardo multimaster and master/slave Postgres replication
rjbs/Dist-Zilla - scary tools for building CPAN distributions
kjellm/munin-mysql - Improved MySQL Graphs for Munin
holygeek/git-number - Use numbers for dealing with files in git
s-aska/dropbox-api-command - Dropbox API wrapper command.
pintsized/ledge - A Lua application for OpenResty, providing scriptable HTTP cache functionality for Nginx.
rcarmo/textwrangler-bbedit-solarized - solarized color scheme for BBEdit and TextWrangler
lamw/vghetto-scripts - Various virtuallyGhetto scripts for VMware based solutions
tokuhirom/Amon - yet another web application framework
cschneid/irclogger - Sinatra based irclogger.com
andrewning/sortphotos - SortPhotos is a Python script that organizes photos and videos into folders using date/time information
pintsized/lua-resty-http - Lua HTTP client cosocket driver for OpenResty / ngx_lua.
jamesc/nagios-plugins-rabbitmq - A set of nagios checks for RabbitMQ using the management interface
kazeburo/cloudforecast - the server metrics gathering
zigdon/twirssi - An irssi script allowing the use of Twitter from within the IRC client.
ganglia/gmetric - Repository of user-contributed gmetric scripts
joemiller/collectd-graphite - collectd plugin for sending data to graphite
naoya/md2inao - Convert markdown to inao-format for WEB+DB PRESS
inverse-inc/packetfence - PacketFence is a fully supported, trusted, Free and Open Source network access control (NAC) solution. Boasting an impressive feature set including a captive-portal for registration and remediation, centralized wired and wireless management, powerful guest management options, 802.1X support, layer-2 isolation of problematic devices; PacketFence can be used to effectively secure networks small to very large heterogeneous networks.
devd/Academic-Writing-Check - check for passive words, weasel words, duplicate words, typographical errors and words strunk & white don't like
yoshinorim/mha4mysql-manager - Development tree of Master High Availability Manager and tools for MySQL (MHA), Manager part
yaoweibin/ngx_http_substitutions_filter_module - a filter module which can do both regular expression and fixed string substitutions for nginx
yaoweibin/nginx_syslog_patch - add the full syslog feature to Nginx
jjl/get_iplayer - A utility for grabbing tv and radio from BBC iPlayer. Phil Lewis has stopped developed it so I've forked it.
kost/dvcs-ripper - Rip web accessible (distributed) version control systems: SVN/GIT/HG...
mrash/fwknop - Single Packet Authorization > Port Knocking
majutsushi/urxvt-font-size - Change the urxvt font size on the fly
apenwarr/gitbuilder - Auto-builds and tests all the branches of your git projects, showing pass/fail results on a web page/RSS feed. Isolates failures to the first commit that caused the problem.
tangledhelix/dotfiles - My dotfiles
shabble/irssi-scripts - Repo to store some personal irssi scripts
kud/jpegrescan - JPEGrescan: losslessly shrink any JPEG file.
gregkh/bti - bash twitter ididocy
woothee/woothee - User-Agent parser/classifier for multi languages
spencertipping/nfu - Numeric Fu for the command line
davidbauer/Instacurate - Turn your Twitter timeline into a personalised news site, in an instant. Fetches links from your timeline and displays them in a discovery friendly design.
yuri-gushin/Roboo - Roboo - HTTP Robot Mitigator
kni/redis-sharding - Redis Sharding is a multiplexed proxy-server, designed to work with the database divided to several servers.
tempire/MojoExample - Mojolicious example with DBIx::Class schema load, deploy, fixtures, and tests.
reyjrar/es-utils - ElasticSearch Utilities
omniti-labs/omnipitr - Advanced WAL File Management Tools for PostgreSQL
GDSSecurity/PadBuster - Automated script for performing Padding Oracle attacks
openresty/rds-json-nginx-module - An nginx output filter that formats Resty DBD Streams generated by ngx_drizzle and others to JSON
zaf/asterisk-speech-recog - Speech recognition script for Asterisk that uses google's speech engine.
Ibmurai/Markdown.codaplugin - A Markdown plugin for Coda.
oetiker/SmokePing - The Active Monitoring System
openresty/lua-resty-upload - Streaming reader and parser for http file uploading based on ngx_lua cosocket
nriley/Pester - Simple, disposable alarms and timers for OS X.
dabockster/Smackbook-Yosemite - Updated Smackbook script for OS X Yosemite
cloudflare/lua-resty-logger-socket - Raw-socket-based Logger Library for Nginx (based on ngx_lua)
simpl/ngx_mongo - Non-blocking upstream module for Nginx to connect to MongoDB
iafan/Hacksby - Description and unofficial implementation of Furby's audio protocol
NixOS/hydra - Hydra, the Nix-based continuous build system
WolverineFan/YNABLinuxInstall - Install script for YNAB 4 on Linux
SPORE/specifications - SPORE specifications
xchataqua/xchataqua - An IRC client, OS X native front-end for XChat ( http://itunes.apple.com/app/id447521961 )
jfrazelle/dotfiles - My dotfiles
ytoolshed/pogo - Pogo is an agent-based system for running interruptive commands safely on thousands of machines in parallel
openresty/lua-resty-websocket - WebSocket support for the ngx_lua module (and OpenResty)
jzawodn/mytop - a "top" clone for MySQL
fonnesbeck/Bios8366 - Advanced Statistical Computing at Vanderbilt University's Department of Biostatistics
dbsrgits/dbix-class - Official github remote for git.shadowcat.co.uk DBIx-Class.git
bricoleurs/bricolage - Content management and publishing system
exflickr/GodAuth - Authentication layer for web app tools
JJ/hoborg - A dieselpunk novel with Spanish-created robot hobos in a balcanized America at the beginning of the XX century
zigdon/xkcd-Bucket - Bucket is the channel bot for #xkcd
jollyjinx/ZFS-TimeMachine - TimeMachine style backup for ZFS
atomia/atomiadns - Atomia DNS
comotion/VSF - Varnish Security Firewall
bgcngm/mtk-tools - Unpack / repack MT65xx/MT83xx boot.img, recovery.img or logo.bin
windytan/redsea - Decoder for FM-RDS.
tudorconstantin/Mojolicious-Boilerplate - The Web in an Awesome Box
openresty/lua-upstream-nginx-module - Nginx C module to expose Lua API to ngx_lua for Nginx upstreams
openresty/test-nginx - Data-driven test scaffold for Nginx C module and OpenResty Lua library development
mndrix/merge-this - Revision control stress tests
brendangregg/HeatMap - Heat map generation tools
crucially/riakfuse - Filesystem backed by riak
DmitryKoterov/dklab_realsync - dkLab RealSync: replicate developer's files over SSH in realtime
xme/pastemon - pastebin.com Content Monitoring Tool

BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): Theory and Application,

Jit — Wed, 23 May 2018 06:54:32 -0500

BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion error.

Here is how I use the blasr to align PacBio reads to the contigs (target.fasta). The “target.fasta.sa” is the suffix array from “target.fasta” generated by sawriter.

blasr query.fa ./target.fasta -sa ./target.fasta.sa -bestn 40 -maxScore -500 -m 4 -nproc 24 -out target.m4 -maxLCPLength 15

the output format option “-m 4″ generate the alignment coordinate. Not fully documented, but I can explain that to you.

I use a 24 cores / 48G ram server for the alignment. It took about 2 to 3 hours aligning 3G PacBio Reads to 10^6 sequences of short read contigs with a mean 3.5kbp length.

Address of the bookmark: http://bix.ucsd.edu/projects/blasr/

AnchorWave

Neel — Wed, 23 Feb 2022 08:14:35 -0600

AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor intervals. By performing sensitive sequence alignment for each shorter interval via a 2-piece affine gap cost strategy and merging them together, AnchorWave generates a whole-genome alignment for each collinear block. AnchorWave implements commands to guide collinear block identification with or without chromosomal rearrangements and provides options to use known polyploidy levels or whole-genome duplications to inform alignment.

Address of the bookmark: https://github.com/baoxingsong/AnchorWave