The tar command is used to rip a collection of files and directories into a highly compressed archive file commonly called tarball or tar, gzip and bzip in Linux.
To create a highly compressed tar file we use the option j. The following example command will create a Phpfiles-org.tar.bz2 file for a directory /home/php. (Note: tar.bz2 and tbz is similar to tb2).
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The tar command is used to put a collection of files and folders into a highly compressed archive file commonly called tarball or tar in Linux. The tar is most widely used command to create compressed archive files and that can be moved easily from one disk to another disk or machine to machine.
The bz2 feature compress and create archive file less than the size of the gzip. The bz2 compression takes more time to compress and decompress files as compared to gzip which takes less time. To create highly compressed tar file we use option as j. The following example command will create a Phpfiles-org.tar.bz2 file for a directory /home/php. (Note: tar.bz2 and tbz is similar as tb2).
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If you want to update a portable installation to a newer version, download the new version in compressed format, then extract the contents in a temporary folder. Now you may either move the "portable" folder you have from the old installation into the new one, or copy all the files of the new version onto the old one, overwriting all the files. Either way you should end up with the updated portable Arduino Software (IDE) installation with your cores, libraries and sketches preserved. Remember to rename the root folder with the proper release version, if needed.You should always launch the executable file "Arduino" from inside the folder of your portable installation to use the sketches, cores and libraries contained in it. If you have another installation of the Arduino Software (IDE) on the machine you are using, that version won't be affected. Libraries and cores already installed on the machine won't be seen or used by the portable installation.
Oracle does not allow downloads without accepting their license, therefore we needed to modify the header of our request. Alternatively, you can just download the compressed file using your browser and manually upload it using a SFTP/FTP client.
As MAF files can be rather large (typically several gigabytes) MafFilter can read and write compressed files, using the zip, gzip and bzip2 compression formats. The compression and decompression is achieved with the boost-iostream library. Practically, the use of compressed files has very little impact on the memory usage or computation speed while reducing considerably the amount of disk space. At the time of writing, the amount of publicly available parsers for MAF files is rather limited. The corresponding classes in the Python language have not yet integrated the stable branch of the BioPython libraries. In order to assess the performance of the Bio++ parser, we therefore compare it to the BioPerl library. The resulting perl script (see Additional file 1) parses the compressed MAF file and outputs for each alignment block with more than a thousand sites the number of sequences, the length of the alignment and the coordinates of the sequence of one species if represented in the alignment block. This simple pipeline allows to directly compare the efficiency of the parsers themselves, as the only computations required are file reading, as well as allocation and initialization of the dedicated structures for storing data into memory. The corresponding MafFilter option file is provided in the example directory of the distributed source code. To compare the two approaches, we used the 46 vertebrates alignment of Human chromosome 22 downloaded from UCSC [8] as input data, and ran the analyses on a linux workstation (Intel(R) Xeon(R) CPU E5520 @ 2.27GHz, with 16Gb of RAM running Ubuntu 12.04). The complete parsing takes 30 minutes with the BioPerl script while it completes in only 3 minutes with MafFilter. MafFilter was used to analyse the complete Gorilla genome aligned with other Primates (2Gb alignment) [9], as well as resequencing data of 27 individual genomes from the fungus Zymoseptoria pseudotritici (40Mb alignment, E. Stukenbrock, pers. communication). 2ff7e9595c
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