https://bioinformaticsonline.com/snippets/view/43295/install-bwise-using-conda? https://bioinformaticsonline.com/snippets/view/43295/install-bwise-using-conda Thu, 19 Aug 2021 09:21:02 -0500 https://bioinformaticsonline.com/snippets/view/43295/install-bwise-using-conda (JitMetaENV) ➜ test_phase_assebly conda install -c bioconda bwise Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - bwise The following packages will be downloaded: package | build ---------------------------|----------------- bcalm-2.2.3 | h2e03b76_2 4.6 MB bioconda bgreat-2.0.0 | h2e03b76_3 143 KB bioconda btrim-1.0.1 | h7d875b9_3 48 KB bioconda bwise-1.0.0 | h2e03b76_1 11 KB bioconda certifi-2021.5.30 | py36h5fab9bb_0 141 KB conda-forge ------------------------------------------------------------ Total: 4.9 MB The following NEW packages will be INSTALLED: bcalm bioconda/linux-64::bcalm-2.2.3-h2e03b76_2 bgreat bioconda/linux-64::bgreat-2.0.0-h2e03b76_3 btrim bioconda/linux-64::btrim-1.0.1-h7d875b9_3 bwise bioconda/linux-64::bwise-1.0.0-h2e03b76_1 The following packages will be UPDATED: ca-certificates 2021.4.13-h06a4308_1 --> 2021.7.5-h06a4308_1 certifi 2020.12.5-py36h5fab9bb_1 --> 2021.5.30-py36h5fab9bb_0 Proceed ([y]/n)? y Downloading and Extracting Packages certifi-2021.5.30 | 141 KB | ####################################################################### | 100% bcalm-2.2.3 | 4.6 MB | ####################################################################### | 100% bwise-1.0.0 | 11 KB | ####################################################################### | 100% btrim-1.0.1 | 48 KB | ####################################################################### | 100% bgreat-2.0.0 | 143 KB | ####################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (JitMetaENV) ➜ test_phase_assebly bwise *** This is BWISE - High order De Bruijn graph assembler *** The command line was: /home/urbe/anaconda3/envs/JitMetaENV/bin/bwise [Warning] /home/urbe/JitSimuStudy/test_phase_assebly directory already exists, BWISE will use it. Results will be stored in: /home/urbe/JitSimuStudy/test_phase_assebly usage: bwise [-h] [-x PAIRED_READFILES] [-u SINGLE_READFILES] [-s KMER_SOLIDITY] [-S KMER_COVERAGE] [-p SR_SOLIDITY] [-P SR_COVERAGE] [-k K_MIN] [-K K_MAX] [-e MAPPING_EFFORT] [-a ANCHOR_SIZE] [-i FRACTION_ANCHOR] [-A MAX_OCCURENCE] [-m MISSMATCH_ALLOWED] [-g GREEDY_K2000] [-t NB_CORES] [-o OUT_DIR] [-H HAPLO_MODE] [--version] [FATAL ERROR] BWISE requires at least a read file To find out why, try `Bwise --help` and/or check the logs files of the various steps of the pipeline (logs/logBloo coo, logs/logBcalm, logs/logTips, logs/logBgreat, logs/logK2000).]]> Jit