Cedric Laczny claczny
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| SHELL := /bin/bash | |
| ##### | |
| # PRESETS | |
| ##### | |
| FASTA?=YOUR-FASTA-FILE.fa | |
| KRAKEN_PATH?=KRAKEN-BINARY-TOP-FOLDER | |
| KRAKEN_CORES?=10 | |
| KRAKEN_FILTER_THRESHOLD?=0.2 |
claczny
/ Makefile.cmp_bash5tools_dextractor
Last active
August 8, 2016 11:24
Makefile to compare bash5tools and dextractor module, both for the extraction of FASTA-formatted reads from PacBio data. Includes downloading of the *large* raw PacBio data
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| SHELL=/bin/bash | |
| MOVIE=m151020_151817_00127_c100889452550000001823187103261622_s1_p0 | |
| FASTA=$(MOVIE).fasta | |
| #QUIVA=$(MOVIE).quiva | |
| BAS_H5=$(MOVIE).bas.h5 | |
| BAX_1_H5=$(MOVIE).1.bax.h5 | |
| BAX_2_H5=$(MOVIE).2.bax.h5 | |
| BAX_3_H5=$(MOVIE).3.bax.h5 | |
| METADATA_XML=$(MOVIE).metadata.xml |
claczny
/ Makefile.pacbio_extract_fasta
Last active
August 8, 2016 09:52
A makefile to extract FASTA sequences from PacBio files using the dextractor module from DAZZLER
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| SHELL=/bin/bash | |
| MOVIE=YOUR_MOVIE_ID | |
| FASTA=$(MOVIE).fasta | |
| #QUIVA=$(MOVIE).quiva | |
| BAS_H5=$(MOVIE).bas.h5 | |
| BAX_1_H5=$(MOVIE).1.bax.h5 | |
| BAX_2_H5=$(MOVIE).2.bax.h5 | |
| BAX_3_H5=$(MOVIE).3.bax.h5 | |
| METADATA_XML=$(MOVIE).metadata.xml |
claczny
/ gist:39bb50364dcfb1b8367e0d5d28cf57e7
Created
June 16, 2016 07:13
Opening iTerm From a Finder Directory
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| on run {input, parameters} | |
| tell application "Finder" | |
| set dir_path to quoted form of (POSIX path of (folder of the front window as alias)) | |
| end tell | |
| CD_to(dir_path) | |
| end run | |
| on CD_to(theDir) | |
| tell application "iTerm" | |
| activate |
claczny
/ Perl-5.18.2-foss-2015b-extended.eb
Created
January 10, 2016 14:21
Extension of the Perl easyconfig to enable installation of LWP, including installation of LWP itself.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name = 'Perl' | |
| version = '5.18.2' | |
| versionsuffix = '-extended' | |
| homepage = 'http://www.perl.org/' | |
| description = """Larry Wall's Practical Extraction and Report Language""" | |
| toolchain = {'name': 'foss', 'version': '2015b'} | |
| toolchainopts = {'optarch': True, 'pic': True} |
claczny
/ HMP_mock_organisms_id.csv
Created
December 16, 2015 10:12
NCBI-related information for HMP mock community http://downloads.hmpdacc.org/data/HMMC/HMPRP_sT1-Mock.pdf
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #ATCC | NCBI taxonomy | Definition | GenBank | Comment | |
|---|---|---|---|---|---|
| ATCC 17978 | 400667 | Acinetobacter baumannii ATCC 17978 | CP000521.1 | ||
| ATCC 17982 | 411466 | Actinomyces odontolyticus ATCC 17982 | AAYI00000000.2 | ||
| ATCC 10987 | 222523 | Bacillus cereus ATCC 10987 | AE017194.1 | ||
| ATCC 8482 | 435590 | Bacteroides vulgatus ATCC 8482 | CP000139.1 | ||
| ATCC MYA-2876 | 237561 | Candida albicans SC5314 | GCA_000182965.2 | ||
| ATCC 51743 | 290402 | Clostridium beijerinckii NCIMB 8052 | CP000721.1 | Found NCBI ID -> Chose 'Identical GenBank Sequence' | |
| DSM 20539 | 243230 | Deinococcus radiodurans R1 | GCA_000008565.1 | ||
| ATCC 47077 | 474186 | Enterococcus faecalis OG1RF | NC_017316.1 | ||
| ATCC 700926 | 511145 | Escherichia coli str. K-12 substr. MG1655 | U00096.3 | Found via http://www.lgcstandards-atcc.org/products/all/700926.aspx?geo_country=de |
NewerOlder