<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/27331?offset=400 https://bioinformaticsonline.com/opportunity/view/22520/recruitment-for-6-positions-of-jrf-junior-research-fellow Thu, 04 Jun 2015 15:22:54 -0500 <![CDATA[RECRUITMENT FOR 6 POSITIONS OF JRF (Junior Research Fellow)]]> Institute of Bioresources and Sustainable Development (IBSD), a National Institute of the Department of Biotechnology, Government of India invites applications for 6 positions of JRF for 2015. The main mandate of IBSD is Conservation and Sustainable Utilization of Bioresources for the Socio-economic Development of the North East Region of India, which is a genetic treasure trove of plants, animals and microbial resources. This region falls among the World’s top 10 Biodiversity Hotspots. The broad areas of research are in Plant Bioresources, Microbial Resources, Natural Product Chemistry, Animal Bioresources and Bioinformatics and Database Management.

Minimum qualifications: M.Sc. with minimum 55% for general and OBD Category (55% for SC/St/PH) in the above-mentioned subject areas (viz. Biotechnology, Life Sciences, Microbiology, Botany, Plant Sciences, Chemistry, Zoology, Animal Sciences, Fishery Sciences and any other relevant branches).

Preference will be given to those holding valid CSIR-UGC NET JRF. DBT-JRF, ICAR-JRF, ICMR-JRF and DST-INSPIRE Fellowship while NET/SLET/SET qualified and GATE qualified candidates (90 or above percentile) are also encouraged to apply. Reservations of seats: 15% for SC, 7.5% for ST, 27% for OBC (noncreamy layer) and 3% for Physically Handicapped as per statutory norms.

Selection Procedure: If the number of JRF and INSPIRE qualified candidates is more, selection will be based on interview of the JRF and INSPIRE qualified candidates only. The selected candidates may be registered for Ph.D. in any of the recognized Universities in India.

Application Procedure: Application should be sent in the prescribed application form (available on the IBSD website). The candidate should send the completed and signed form along with self attested copies of all supporting certificates and marksheets along with an application fee of Rs.300/- (For GEN/OBC/PH) & Rs.150/- for (SC/ST), for which a Demand Draft in favour of ‘Institute of Bioresources and Sustainable Development, payable at Imphal, Manipur, should be attached with the application form. Candidates are advised to provide their email ID and mobile number as they would be contacted electronically by the Institute. Duly filled applications (with ‘Application for IBSD PhD Programme’ super scribed on the envelope) should be sent to ‘The Director, Institute of Bioresources and Sustainable Development, Takyelpat, Imphal-795001, Manipur so as to reach on or before 6th of July, 2015. Applications send by email with scan copy of required enclosures will also be accepted and can be sent to director.ibsd@nic.in. However, in such instances, the application will be processed only after the receipt of the mailed hard copies.

Advertisement: http://ibsd.gov.in/jobs/phd_2015/IBSD_JRF_2015.pdf

Application Form : http://ibsd.gov.in/jobs/phd_2015/APPLICATION_FORM.pdf

]]> https://bioinformaticsonline.com/bookmarks/view/44641/heliano-a-fast-and-accurate-tool-for-detection-of-helitron-like-elements Tue, 13 Aug 2024 07:16:34 -0500 https://bioinformaticsonline.com/bookmarks/view/44641/heliano-a-fast-and-accurate-tool-for-detection-of-helitron-like-elements <![CDATA[HELIANO: A fast and accurate tool for detection of Helitron-like elements]]> Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging to identify. Here, we propose HELIANO (Helitron-like elements annotator) as an efficient solution for detecting Helitron-like elements.

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae679/7730539?login=true

Address of the bookmark: https://github.com/Zhenlisme/heliano/

]]> LEGE https://bioinformaticsonline.com/pages/view/22567/rosalind-problem-solution-with-perl Tue, 09 Jun 2015 23:35:18 -0500 https://bioinformaticsonline.com/pages/view/22567/rosalind-problem-solution-with-perl <![CDATA[Rosalind Problem Solution with Perl]]> Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works.

Bioinformatics Textbook Track

Find more about Rosalind puzzle at http://rosalind.info/problems/list-view/?location=bioinformatics-textbook-track

I will provide solution of all the Rosalind problem with Perl for community.

Check out the right sidebar for more links ...

]]> Jit https://bioinformaticsonline.com/blog/view/45177/installing-crossroad-on-ubuntu Fri, 29 May 2026 05:19:45 -0500 https://bioinformaticsonline.com/blog/view/45177/installing-crossroad-on-ubuntu <![CDATA[Installing croSSRoad on Ubuntu !]]> (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
libarrow-compute 3.0MB @ 1.9MB/s 1.6s
orc 1.5MB @ 2.8MB/s 0.5s
libparquet 1.4MB @ 3.1MB/s 0.5s
pip 1.2MB @ 2.9MB/s 0.4s
libabseil 1.4MB @ 2.2MB/s 0.6s
pillow 1.1MB @ 2.7MB/s 0.4s
libsqlite 955.0kB @ 2.9MB/s 0.3s
libgoogle-cloud-storage 779.6kB @ 2.7MB/s 0.3s
fonttools 846.0kB @ 2.1MB/s 0.4s
libopentelemetry-cpp 934.3kB @ 1.8MB/s 0.5s
libarrow-acero 592.3kB @ 2.2MB/s 0.2s
uvloop 593.4kB @ 1.3MB/s 0.4s
libarrow-dataset 592.2kB @ 2.7MB/s 0.2s
libarrow-substrait 501.9kB @ 1.8MB/s 0.2s
azure-storage-blobs-cpp 587.1kB @ 1.6MB/s 0.3s
libthrift 423.9kB @ 2.8MB/s 0.2s
crossroad 1.8MB @ 663.3kB/s 2.6s
libuv 419.9kB @ 2.3MB/s 0.2s
fastar 423.4kB @ 966.7kB/s 0.3s
aws-crt-cpp 412.5kB @ 2.9MB/s 0.1s
watchfiles 415.6kB @ 1.6MB/s 0.3s
unicodedata2 409.6kB @ 1.8MB/s 0.2s
libopentelemetry-cpp-headers 396.4kB @ 2.2MB/s 0.2s
s2n 388.1kB @ 2.5MB/s 0.1s
brotli-python 367.4kB @ 1.7MB/s 0.1s
websockets 383.0kB @ 1.3MB/s 0.3s
azure-core-cpp 348.7kB @ 2.7MB/s 0.1s
pydantic 346.5kB @ 1.9MB/s 0.2s
contourpy 324.0kB @ 2.3MB/s 0.1s
libpng 317.7kB @ 1.8MB/s 0.2s
azure-storage-files-datalake-cpp 303.8kB @ 1.9MB/s 0.1s
narwhals 284.3kB @ 1.8MB/s 0.2s
fontconfig 280.9kB @ 866.6kB/s 0.2s
python 36.7MB @ 3.0MB/s 12.0s
azure-identity-cpp 250.5kB @ 1.5MB/s 0.1s
lcms2 251.1kB @ 2.0MB/s 0.1s
aws-c-common 242.3kB @ 2.8MB/s 0.1s
libre2-11 213.1kB @ 66.4kB/s 0.1s
aws-c-http 230.3kB @ 1.7MB/s 0.1s
aws-c-mqtt 221.7kB @ 307.2kB/s 0.1s
sqlite 205.4kB @ ??.?MB/s 0.1s
perf_ssr 720.0kB @ 247.3kB/s 2.3s
prometheus-cpp 199.5kB @ 962.8kB/s 0.1s
pyyaml 202.4kB @ 1.6MB/s 0.1s
typer 184.4kB @ 1.9MB/s 0.1s
aws-c-io 181.6kB @ 1.9MB/s 0.1s
aws-c-s3 153.0kB @ 2.2MB/s 0.1s
azure-storage-common-cpp 159.1kB @ 1.8MB/s 0.1s
expat 148.2kB @ ??.?MB/s 0.0s
anyio 146.8kB @ 2.2MB/s 0.1s
glog 143.5kB @ 2.6MB/s 0.1s
seqtk 141.8kB @ 1.8MB/s 0.1s
nlohmann_json 136.2kB @ 2.1MB/s 0.1s
aws-c-auth 134.4kB @ 1.5MB/s 0.1s
certifi 134.2kB @ 1.8MB/s 0.1s
click 105.0kB @ 1.5MB/s 0.1s
gflags 119.7kB @ 148.2kB/s 0.1s
urllib3 103.6kB @ ??.?MB/s 0.0s
aws-checksums 101.6kB @ ??.?MB/s 0.0s
fastapi-core 95.5kB @ ??.?MB/s 0.0s
libmpdec 92.4kB @ ??.?MB/s 0.0s
packaging 91.6kB @ ??.?MB/s 0.0s
libutf8proc 86.0kB @ ??.?MB/s 0.0s
kiwisolver 77.4kB @ ??.?MB/s 0.0s
libexpat 77.3kB @ 885.4kB/s 0.1s
pydantic-extra-types 73.9kB @ ??.?MB/s 0.0s
markdown-it-py 69.0kB @ ??.?MB/s 0.0s
requests 68.7kB @ ??.?MB/s 0.0s
rich-click 64.4kB @ ??.?MB/s 0.0s
aws-c-event-stream 59.3kB @ ??.?MB/s 0.0s
starlette 63.7kB @ ??.?MB/s 0.0s
aws-c-sdkutils 59.1kB @ ??.?MB/s 0.0s
aws-c-cal 56.9kB @ ??.?MB/s 0.0s
idna 56.9kB @ ??.?MB/s 0.0s
uvicorn 56.3kB @ ??.?MB/s 0.0s
pydantic-settings 52.3kB @ ??.?MB/s 0.0s
email-validator 46.8kB @ ??.?MB/s 0.0s
libuuid 40.2kB @ ??.?MB/s 0.0s
h11 39.1kB @ ??.?MB/s 0.0s
python-multipart 37.8kB @ ??.?MB/s 0.0s
rich-toolkit 32.9kB @ ??.?MB/s 0.0s
upsetplot 28.0kB @ ??.?MB/s 0.0s
libstdcxx-ng 27.8kB @ ??.?MB/s 0.0s
libgfortran 27.7kB @ ??.?MB/s 0.0s
re2 27.5kB @ ??.?MB/s 0.0s
markupsafe 27.4kB @ ??.?MB/s 0.0s
pyarrow 26.8kB @ ??.?MB/s 0.0s
aws-c-compression 22.0kB @ ??.?MB/s 0.0s
tomli 21.6kB @ ??.?MB/s 0.0s
typing-inspection 20.9kB @ ??.?MB/s 0.0s
fastapi-cli 18.9kB @ ??.?MB/s 0.0s
libblas 18.8kB @ ??.?MB/s 0.0s
httptools 99.0kB @ ??.?MB/s 0.4s
liblapack 18.8kB @ ??.?MB/s 0.0s
libcblas 18.8kB @ ??.?MB/s 0.0s
email_validator 7.1kB @ ??.?MB/s 0.0s
backports.zstd 7.5kB @ ??.?MB/s 0.0s
python_abi 7.0kB @ ??.?MB/s 0.0s
fastapi 4.8kB @ ??.?MB/s 0.0s
uvicorn-standard 4.1kB @ ??.?MB/s 0.0s
rich-argparse 26.8kB @ ??.?MB/s 0.2s
plotly-upset-hd 356.0kB @ 181.5kB/s 1.8s
Linking seqkit-2.13.0-he881be0_0
Linking bedtools-2.31.1-h13024bc_3
Linking seqtk-1.5-h577a1d6_1
Linking libuuid-2.42.1-h5347b49_0
Linking readline-8.3-h853b02a_0
Linking libexpat-2.8.1-hecca717_0
Linking nspr-4.38-h29cc59b_0
Linking mathjax-2.7.7-ha770c72_3
Linking libuv-1.52.1-h280c20c_0
Linking yaml-0.2.5-h280c20c_3
Linking ld_impl_linux-64-2.45.1-default_hbd61a6d_102
Linking libmpdec-4.0.0-hb03c661_1
Linking libwebp-base-1.6.0-hd42ef1d_0
Linking zlib-ng-2.3.3-hceb46e0_1
Linking libstdcxx-ng-15.2.0-hdf11a46_19
Linking pthread-stubs-0.4-hb9d3cd8_1002
Linking xorg-libxau-1.0.12-hb03c661_1
Linking xorg-libxdmcp-1.1.5-hb03c661_1
Linking libgfortran5-15.2.0-h68bc16d_19
Linking libpng-1.6.58-h421ea60_0
Linking libbrotlicommon-1.2.0-hb03c661_1
Linking libjpeg-turbo-3.1.4.1-hb03c661_0
Linking libdeflate-1.25-h17f619e_0
Linking lerc-4.1.0-hdb68285_0
Linking libsqlite-3.53.1-h0c1763c_0
Linking libffi-3.5.2-h3435931_0
Linking tk-8.6.13-noxft_h366c992_103
Linking azure-core-cpp-1.16.2-h206d751_0
Linking libabseil-20260107.1-cxx17_h7b12aa8_0
Linking libutf8proc-2.11.3-hfe17d71_0
Linking libopentelemetry-cpp-headers-1.26.0-ha770c72_0
Linking zlib-1.3.2-h25fd6f3_2
Linking snappy-1.2.2-h03e3b7b_1
Linking nlohmann_json-3.12.0-h54a6638_1
Linking aws-c-common-0.13.1-hb03c661_0
Linking s2n-1.7.3-hc5a330e_0
Linking gflags-2.2.2-h5888daf_1005
Linking libevent-2.1.12-hf998b51_1
Linking expat-2.8.1-hecca717_0
Linking libcrc32c-1.1.2-h9c3ff4c_0
Linking qhull-2020.2-h434a139_5
Linking libxcb-1.17.0-h8a09558_0
Linking libgfortran-15.2.0-h69a702a_19
Linking libfreetype6-2.14.3-h73754d4_0
Linking libbrotlienc-1.2.0-hb03c661_1
Linking libbrotlidec-1.2.0-hb03c661_1
Linking libtiff-4.7.1-h9d88235_1
Linking sqlite-3.53.1-hbc0de68_0
Linking nss-3.118-h445c969_0
Linking azure-identity-cpp-1.13.3-hed0cdb0_1
Linking azure-storage-common-cpp-12.13.0-ha7a2c86_0
Linking libprotobuf-6.33.5-h6eeba95_1
Linking libre2-11-2025.11.05-h0dc7533_1
Linking prometheus-cpp-1.3.0-ha5d0236_0
Linking aws-c-compression-0.3.2-h16e98cb_1
Linking aws-checksums-0.2.10-h16e98cb_1
Linking aws-c-sdkutils-0.2.4-h16e98cb_5
Linking aws-c-cal-0.9.14-h8e43964_1
Linking glog-0.7.1-hbabe93e_0
Linking libthrift-0.22.0-h7d032f7_2
Linking libopenblas-0.3.33-pthreads_h94d23a6_0
Linking libfreetype-2.14.3-ha770c72_0
Linking brotli-bin-1.2.0-hb03c661_1
Linking lcms2-2.19.1-h0c24ade_0
Linking openjpeg-2.5.4-h55fea9a_0
Linking azure-storage-blobs-cpp-12.17.0-hf824e48_1
Linking re2-2025.11.05-h5301d42_1
Linking aws-c-io-0.26.3-h955231c_3
Linking libblas-3.11.0-8_h4a7cf45_openblas
Linking fontconfig-2.18.0-h27c8c51_0
Linking freetype-2.14.3-ha770c72_0
Linking brotli-1.2.0-hed03a55_1
Linking azure-storage-files-datalake-cpp-12.15.0-h1e5b466_0
Linking libgrpc-1.78.1-h1d1128b_0
Linking aws-c-event-stream-0.7.1-h9be7a74_1
Linking aws-c-http-0.11.0-hcbcd92d_1
Linking libcblas-3.11.0-8_h0358290_openblas
Linking liblapack-3.11.0-8_h47877c9_openblas
Linking libopentelemetry-cpp-1.26.0-h9692893_0
Linking aws-c-auth-0.10.3-h3aafcba_1
Linking aws-c-mqtt-0.15.2-h8af55cf_3
Linking libgoogle-cloud-3.5.0-h25dbb67_0
Linking aws-c-s3-0.12.3-h00bea6e_2
Linking libgoogle-cloud-storage-3.5.0-hdbdcf42_0
Linking aws-crt-cpp-0.38.3-h7b0d4b4_2
Linking aws-sdk-cpp-1.11.747-h5a171d8_5
Linking python_abi-3.14-8_cp314
Linking font-ttf-dejavu-sans-mono-2.37-hab24e00_0
Linking tzdata-2025c-hc9c84f9_1
Linking font-ttf-ubuntu-0.83-h77eed37_3
Linking font-ttf-inconsolata-3.000-h77eed37_0
Linking font-ttf-source-code-pro-2.038-h77eed37_0
Linking fonts-conda-forge-1-hc364b38_1
Linking orc-2.3.0-h21090e2_0
Linking python-3.14.5-habeac84_100_cp314
Linking kaleido-core-0.2.1-h3644ca4_0
Linking libarrow-24.0.0-h6f10b76_3_cpu
Linking libparquet-24.0.0-h7376487_3_cpu
Linking libarrow-compute-24.0.0-h53684a4_3_cpu
Linking libarrow-acero-24.0.0-h635bf11_3_cpu
Linking libarrow-dataset-24.0.0-h635bf11_3_cpu
Linking libarrow-substrait-24.0.0-hb4dd7c2_3_cpu
Linking pip-26.1.1-pyh145f28c_0
Linking tomli-2.4.1-pyhcf101f3_0
Linking six-1.17.0-pyhe01879c_1
Linking pysocks-1.7.1-pyha55dd90_7
Linking hyperframe-6.1.0-pyhd8ed1ab_0
Linking hpack-4.1.0-pyhd8ed1ab_0
Linking backports.zstd-1.5.0-py314h680f03e_0
Linking pyparsing-3.3.2-pyhcf101f3_0
Linking cycler-0.12.1-pyhcf101f3_2
Linking sniffio-1.3.1-pyhd8ed1ab_2
Linking mdurl-0.1.2-pyhd8ed1ab_1
Linking narwhals-2.21.2-pyhcf101f3_0
Linking packaging-26.2-pyhc364b38_0
Linking charset-normalizer-3.4.7-pyhd8ed1ab_0
Linking certifi-2026.5.20-pyhd8ed1ab_0
Linking idna-3.17-pyhcf101f3_0
Linking pygments-2.20.0-pyhd8ed1ab_0
Linking shellingham-1.5.4-pyhd8ed1ab_2
Linking annotated-doc-0.0.4-pyhcf101f3_0
Linking colorama-0.4.6-pyhd8ed1ab_1
Linking typing_extensions-4.15.0-pyhcf101f3_0
Linking click-8.4.1-pyhc90fa1f_0
Linking tqdm-4.67.3-pyh8f84b5b_0
Linking python-kaleido-0.2.1-pyhd8ed1ab_0
Linking python-multipart-0.0.29-pyhcf101f3_0
Linking python-dotenv-1.2.2-pyhcf101f3_0
Linking argcomplete-3.6.3-pyhd8ed1ab_0
Linking python-dateutil-2.9.0.post0-pyhe01879c_2
Linking h2-4.3.0-pyhcf101f3_0
Linking dnspython-2.8.0-pyhcf101f3_0
Linking markdown-it-py-4.2.0-pyhd8ed1ab_0
Linking plotly-6.6.0-pyhd8ed1ab_0
Linking exceptiongroup-1.3.1-pyhd8ed1ab_0
Linking typing-inspection-0.4.2-pyhcf101f3_2
Linking typing-extensions-4.15.0-h396c80c_0
Linking h11-0.16.0-pyhcf101f3_1
Linking email-validator-2.3.0-pyhd8ed1ab_0
Linking rich-15.0.0-pyhcf101f3_0
Linking anyio-4.13.0-pyhcf101f3_0
Linking annotated-types-0.7.0-pyhd8ed1ab_1
Linking uvicorn-0.48.0-pyhc90fa1f_0
Linking email_validator-2.3.0-hd8ed1ab_0
Linking rich-toolkit-0.19.10-pyhcf101f3_0
Linking typer-0.26.3-pyhcf101f3_0
Linking rich-click-1.9.8-pyh8f84b5b_0
Linking rich-argparse-1.8.0-pyhd8ed1ab_0
Linking httpcore-1.0.9-pyh29332c3_0
Linking starlette-1.1.0-pyhcf101f3_0
Linking httpx-0.28.1-pyhd8ed1ab_0
Linking pyarrow-core-24.0.0-py314h969be7f_0_cpu
Linking unicodedata2-17.0.1-py314h5bd0f2a_0
Linking brotli-python-1.2.0-py314h3de4e8d_1
Linking pillow-12.2.0-py314h8ec4b1a_0
Linking kiwisolver-1.5.0-py314h97ea11e_0
Linking fastar-0.11.0-py314h0b738fb_0
Linking markupsafe-3.0.3-py314h67df5f8_1
Linking websockets-16.0-py314h0f05182_1
Linking uvloop-0.22.1-py314h5bd0f2a_1
Linking pyyaml-6.0.3-py314h67df5f8_1
Linking httptools-0.7.1-py314h5bd0f2a_1
Linking numpy-2.4.6-py314h2b28147_0
Linking pydantic-core-2.46.4-py314h2e6c369_0
Linking watchfiles-1.2.0-py314ha5689aa_0
Linking pyarrow-24.0.0-py314hdafbbf9_0
Linking contourpy-1.3.3-py314h97ea11e_4
Linking biopython-1.87-py314h5bd0f2a_0
Linking pandas-3.0.3-py314hb4ffadd_0
Linking munkres-1.0.7-py_1
Linking urllib3-2.7.0-pyhd8ed1ab_0
Linking jinja2-3.1.6-pyhcf101f3_1
Linking pydantic-2.13.4-pyhcf101f3_0
Linking uvicorn-standard-0.48.0-he364bde_0
Linking fonttools-4.63.0-pyh7db6752_0
Linking requests-2.34.2-pyhcf101f3_0
Linking pydantic-settings-2.14.1-pyhcf101f3_0
Linking pydantic-extra-types-2.11.2-pyhcf101f3_0
Linking fastapi-core-0.136.3-pyhcf101f3_0
Linking fastapi-cli-0.0.23-pyhcf101f3_0
Linking fastapi-0.136.3-h5ddb490_0
Linking plotly-upset-hd-0.0.2-py_0
Linking matplotlib-base-3.10.9-py314h1194b4b_0
Linking upsetplot-0.9.0-pyhd8ed1ab_1
Linking perf_ssr-0.4.8-py_0
Linking crossroad-0.3.6-pyh7e60211_0

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$

 

]]> ComBioX https://bioinformaticsonline.com/opportunity/view/22616/research-associate-manit-allahabad-uttar-pradesh Fri, 12 Jun 2015 05:44:38 -0500 <![CDATA[Research Associate MANIT - Allahabad, Uttar Pradesh]]> Applications are invited from Indian nationals for the post of Research Assistant (on contract) in research project entitled “Identification of novel drug targets in Aspergillus fumigatus genome prioritized by essentiality based screening and rational designing of new antifungal compounds” sanction order no. CST/238 dated 12/05/2015 sponsored by Council of Science and Technology U.P.

The duly completed application on prescribed format along with copies of supporting documents must reach to: Office of the Dean (Research & Consultancy), Motilal Nehru National Institute of Technology, Allahabad-211004 on or before 03/07/2015.

The position is purely temporary and will be governed by the funding agency rules & service conditions of Office of the Dean (Research & Consultancy), MNNIT Allahabad.

For detail advertisement see: www.mnnit.ac.in/images/newstories/Advertisement_for_the_post_of_Research_Assistant_in_UPCST_Project_of_Biotechnology_Department.pdf

]]> https://bioinformaticsonline.com/opportunity/view/22779/research-associate-at-international-centre-for-genetic-engineering-and-biotechnology-icgeb Wed, 17 Jun 2015 18:49:05 -0500 <![CDATA[Research Associate at International Centre for Genetic Engineering and Biotechnology (ICGEB)]]> Research Associate
International Centre for Genetic Engineering and Biotechnology (ICGEB)
Address: Aruna Asaf Ali Marg, Jawaharlal Nehru University, New Delhi
Postal Code: 110067
City: New Delhi
State: Delhi
Qualifications: Experience in many docking softwares and operating systems is essential. Additional experience in bioinformatics and computational biology tools will be useful.
Details will be available at: http://www.icgeb.org/vacancies.html

How To Apply: Submit curriculum vitae to: sb.icgeb@gmail.com
Last Date: 5 July 2015

]]> https://bioinformaticsonline.com/opportunity/view/22788/research-associate-bioinformatics-job-position-in-indian-agricultural-statistics-research-institute-iasri-pusa-new-delhi Wed, 17 Jun 2015 20:48:40 -0500 <![CDATA[Research Associate Bioinformatics job position in Indian Agricultural Statistics Research Institute (IASRI), Pusa, New Delhi]]> Research Associate Statistics

Eligibility : M Phil / Phd, MSc

Location : Delhi

Last Date : 27 Jun 2015

Hiring Process : Walk - In
Indian Agricultural Statistics Research Institute (IASRI) - Job DetailsDate of posting:03 Jun 15

Research Associate Statisticsjob position in Indian Agricultural Statistics Research Institute (IASRI)
on purely contractual temporary basis

Project : “ICAR-Network Project of Transgenic in Crops”

Qualification : Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Life Science/ Biotechnology/ Agricultural Science or equivalent OR Post-Graduation in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Life Science/ Biotechnology/ Agricultural Science or equivalent with 1st Division or 60% marks or equivalent with at least two years of research experience.

No.of Post: 01

Emoluments for RA: Consolidated Rs. 24000/- per month + 30% HRA for Ph.D holders and consolidated Rs. 23000/- per month + 30% HRA for Master Degree.

Age Limit : 40 years
How to apply

Walk-in-interview will be held on 27th June 2015, 10.30 A.M at IASRI, Pusa, New Delhi

More at http://iasri.res.in/employment/employment.htm

]]> https://bioinformaticsonline.com/opportunity/view/22944/icgeb-bioinformatics-research-associate-vacancy Thu, 25 Jun 2015 20:41:00 -0500 <![CDATA[ICGEB Bioinformatics Research Associate Vacancy]]> Research Associate Position at ICGEB, New Delhi with Dr. Amit Sharma

Starting 15th July 2015, the position relates to a project specifically for in silico drug docking, screening, design, optimisation and linkage with active chemists.

Experience in many docking softwares and operating systems is essential.

Additional experience in bioinformatics and computational biology tools will be useful.

Submit curriculum vitae to: sb.icgeb@gmail.com

Closing date: 5 July 2015

]]> https://bioinformaticsonline.com/opportunity/view/23384/research-scientist-at-dupont Fri, 17 Jul 2015 20:36:17 -0500 <![CDATA[Research Scientist at DuPONT]]> Research Scientist
Hyderabad, Telangana
Job Description

Job Description

The Global Trait Discovery Informatics (GTDI) group located at the DuPont Knowledge Centre (DKC), Hyderabad, India is currently seeking applications for a highly motivated computational biologist. The GTDI group contributes to research programs in plant biotechnology at the DKC as well as across research centers located in DuPont Pioneer, Johnston, Iowa and at the DuPont Experimental Station in Wilmington, Delaware.

We are looking for candidates who have experience in analysis of high-throughput -omics datasets. The researcher will be primarily responsible for analyzing diverse -omics datatypes, such as transcriptomics, proteomics and metabolomics and actively contribute towards building streamlined solutions.

The candidate will be part of a diverse team of experimental biologists, computational biologists and software developers. A critical aspect of this position involves working with global teams across multiple locations and will require effective project coordination and communication skills. This is an exciting opportunity for candidates with strong data driven skills, who want to work at the interface of computational and experimental biology and contribute towards scientific discovery.

Responsibilities

·Integrate and analyze multiple datatypes in the context of experimental observations with a goal towards formulating testable hypothesis.

·Understanding the research questions from experimental biologists and formulate relevant in silico analyses.

·Establish and implement systematic analysis workflows starting from processing of raw data to biological interpretation.

·Critically analyze a wide variety of experimental data with a view to solving the underlying research questions.

·Identify and generate datasets for scientific testing and evaluation of algorithms.

Qualifications

PhD in computational biology, bioinformatics, population genetics, complex systems, computer sciences or any relevant physical or mathematical sciences, with experience in analyzing diverse -omics datasets.

Job Qualifications

Qualifications

PhD in computational biology, bioinformatics, population genetics, complex systems, computer sciences or any relevant physical or mathematical sciences, with experience in analyzing diverse -omics datasets.

More at http://careers.dupont.com/jobsearch/job-details/research-scientist/006077W-01/

]]> https://bioinformaticsonline.com/opportunity/view/23247/ra-at-csir-urdip Fri, 10 Jul 2015 18:34:03 -0500 <![CDATA[RA at CSIR-URDIP]]> CSIR - UNIT FOR RESEARCH AND DEVELOPMENT OF INFORMATION PRODUCTS (CSIR- URDIP)

Adv. No. URDIP/ 15/2015

Opportunity for young Bioinformatics Professionals to make a career in the area of Intellectual Property

CSIR has set up a Unit for Research and Development of Information Products (CSIRURDIP) at Pune to work in the area of scientific informatics. One of the major focus areas of research work at CSIR-URDIP is PATENT INFORMATICS. With the increasing applications of Bioinformatics in the areas of life sciences industry such as Agriculture and Health Care (Diagnostics and Drugs), the output of research in these area is being protected by different forms of Intellectual Property rights. Realizing the importance of IP in the Bioinformatics field, Department of Biotechnology (DBT) has sanctioned a project on “Development, Facilitation and Harvesting of Bioinformatics related Intellectual Property” at CSIR-URDIP.

The project will involve application of Patent Informatics tools and techniques to Bioinformatics (including creation of patent landscapes, preparation of techno-legal reports of patentability, freedom to operate studies) to help protect IPRs and develop and conduct training programmes on IPRs related to Bioinformatics.

CSIR-URDIP invites applications from young Bioinformatics professionals to work on this emerging area which offers challenging opportunities and attractive career possibilities in future.

Position I: Research Associate

No of Positions: One

Consolidated amount Payable: = Rs 26,400.00

Qualification: PhD in Bioinformatics. In exceptional cases, candidature of M. Tech. candidates with First class in Bioinformatics with three years of relevant work experience will also be considered.

Job requirement: The prospective candidate will be expected to identify patents/scientific literature in field of Bioinformatics, evaluate them Vis a Vis other patents in fields and come up landscape / FTO / Patentability reports.

Age Limit: 35 years.

The candidates meeting the above criteria may appear for walk in interview at their cost on Monday 13th July 2015 at 02:00 p.m. with the CV and supporting documents (original plus copies) at the following address: CSIR Unit or Research and Development of Information Products (URDIP), "Tapovan" S.No. 113 & 114, Near NCL Colony Baner Side Gate, NCL Estate, Pashan Road, Pune-411008, Maharashtra, India

Advertisement: www.urdip.res.in/download/DBT_RA_Advt_July%202015.pdf

]]>