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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/44213?offset=70</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/38765/list-of-tools-frequently-used-while-genome-assembly</guid>
	<pubDate>Tue, 22 Jan 2019 09:39:02 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/38765/list-of-tools-frequently-used-while-genome-assembly</link>
	<title><![CDATA[List of tools frequently used while genome assembly]]></title>
	<description><![CDATA[<h4>List of tools frequently used while genome assembly:</h4><p>I have used the following assemblers</p><ul>
<li><a href="http://bioinf.spbau.ru/spades">Spades</a>&nbsp;(v. 3.10.1)</li>
<li><a href="http://canu.readthedocs.io/en/stable/index.html">CANU</a>&nbsp;(v. 1.6)</li>
<li><a href="https://github.com/rrwick/Unicycler">Unicycler&nbsp;</a>(v. v0.4.1)</li>
<li><a href="https://github.com/lh3/miniasm">Miniasm</a>&nbsp;(v. 0.2-r137-dirty)</li>
</ul><p>I have used the following mappers</p><ul>
<li><a href="https://github.com/lh3/minimap2">minimap2</a>&nbsp;(v.&nbsp;2.0rc1-r232)</li>
<li><a href="https://github.com/lh3/minimap">minimap&nbsp;</a>(v. 0.2-r124-dirty)</li>
<li><a href="https://github.com/lh3/bwa">bwa</a>&nbsp;(v.&nbsp;0.7.12-r1039)</li>
</ul><p>I have used the following polishing tools</p><ul>
<li><a href="https://github.com/isovic/racon">Racon</a>&nbsp;(v. not available)</li>
<li><a href="https://github.com/broadinstitute/pilon">Pilon</a>&nbsp;(v. 1.18)</li>
<li><a href="https://github.com/jts/nanopolish">Nanopolish</a>&nbsp;(v. 0.8.3)</li>
</ul><p>I have used the following tools to assess genome assembly characteristics</p><ul>
<li><a href="https://github.com/chjp/ANI">ANI.pl</a>&nbsp;(https://github.com/chjp/ANI)</li>
<li><a href="http://ecogenomics.github.io/CheckM/">CheckM</a>&nbsp;(v. 1.0.7)</li>
<li><a href="https://github.com/tseemann/prokka">Prokka</a>&nbsp;(v. 1.12)</li>
<li><a href="http://bioinf.spbau.ru/en/quast">QUAST</a>&nbsp;(v. 2.3)</li>
<li><a href="http://mummer.sourceforge.net/">mummer&nbsp;</a>(v. not available)</li>
</ul><p>If you have any ideas or superior tools we have missed please let us know in the comments.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41559/dahak-benchmarking-and-containerization-of-tools-for-analysis-of-complex-non-clinical-metagenomes</guid>
	<pubDate>Thu, 09 Apr 2020 04:56:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41559/dahak-benchmarking-and-containerization-of-tools-for-analysis-of-complex-non-clinical-metagenomes</link>
	<title><![CDATA[Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.]]></title>
	<description><![CDATA[<p><span>Dahak is a software suite that integrates state-of-the-art open source tools for metagenomic analyses. Tools in the dahak software suite will perform various steps in metagenomic analysis workflows including data pre-processing, metagenome assembly, taxonomic and functional classification, genome binning, and gene assignment. We aim to deliver the analytical framework as a robust and reliable containerized workflow system, which will be free from dependency, installation, and execution problems typically associated with other open-source bioinformatics solutions. This will maximize the transparency, data provenance (i.e., the process of tracing the origins of data and its movement through the workflow), and reproducibility.</span></p>
<p><span>More at&nbsp;<a href="https://dahak-metagenomics.github.io/dahak/">https://dahak-metagenomics.github.io/dahak/</a></span></p><p>Address of the bookmark: <a href="https://github.com/dahak-metagenomics/dahak" rel="nofollow">https://github.com/dahak-metagenomics/dahak</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/42275/frequent-parameters-for-bioinformatics-tools</guid>
	<pubDate>Tue, 27 Oct 2020 19:42:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/42275/frequent-parameters-for-bioinformatics-tools</link>
	<title><![CDATA[Frequent parameters for bioinformatics tools !]]></title>
	<description><![CDATA[<div><div>Third party executable parameters and options.</div><div>&nbsp;</div><div>Trimmomatic</div><div>&nbsp;</div><div>&ldquo;ILLUMINACLIP:...:2:30:10&rdquo;</div><div>&ldquo;LEADING:15&rdquo;</div><div>&ldquo;TRAILING:15&rdquo;</div><div>&ldquo;SLIDINGWINDOW:4:20&rdquo;</div><div>&ldquo;MINLEN:20&rdquo;</div><div>&ldquo;TOPHRED33&rdquo;</div><div>&nbsp;</div><div>Filtlong</div><div>--min_length 500</div><div>--min_mean_q 85</div><div>--min_window_q 65</div><div>&nbsp;</div><div>FastQ Screen</div><div>--aligner bowtie2' (bwa for PacBio)</div><div>--subset 1000 (for PacBio)</div><div>&nbsp;</div><div>SPAdes</div><div>--careful</div><div>--disable-gzip-output</div><div>--cov-cutoff auto</div><div>--phred-offset 33</div><div>&nbsp;</div><div>HGAP</div><div>Pbalign.task_options.min_accuracy: 70</div><div>Pbalign.task_options.no_split_subreads: false</div><div>Genomic_consensus.task_options.min_confidence: 40</div><div>falcon_ns.task_options.HGAP_GenomeLength_str:</div><div>6000000</div><div>Pbcoretools.task_options.read_length: 0</div><div>Genomic_consensus.task_options.use_score: 0</div><div>Pbalign.task_options.min_length: 50</div><div>Pbalign.task_options.algorithm_options: --minMatch 12</div><div>--bestn 10 --minPctSimilarity 70.0</div><div>Pbalign.task_options.hit_policy: randombest</div><div>Pbcoretools.task_options.other_filters: rq &gt;= 0.7</div><div>Pbalign.task_options.concordant: false</div><div>Genomic_consensus.task_options.min_coverage: 5</div><div>falcon_ns.task_options.HGAP_SeedCoverage_str: 30</div><div>falcon_ns.task_options.HGAP_AggressiveAsm_bool: false</div><div>Genomic_consensus.task_options.algorithm: best</div><div>falcon_ns.task_options.HGAP_SeedLengthCutoff_str: -1</div><div>Genomic_consensus.task_options.diploid: false</div><div>&nbsp;</div><div>MeDuSa</div><div>-random 100</div><div>&nbsp;</div><div>Prokka</div><div>--usegenus</div><div>--force</div><div>--addgenes</div><div>--rfam</div><div>--rawproduct</div><div>&nbsp;</div><div>cmsearch (taxonomy, 16S)</div><div>--rfam</div><div>--noali</div><div>&nbsp;</div><div>blastn (taxonomy, 16S)</div><div>-evalue 1E-10</div><div>&nbsp;</div><div>blastn (MLST)</div><div>-ungapped</div></div><div><div>-dust no</div><div>-evalue 1E-20</div><div>-word_size 32</div><div>-culling_limit 2</div><div>-perc_identity 95</div><div>&nbsp;</div><div>blastp (VF)</div><div>-culling_limit 2</div><div>&nbsp;</div><div>RGI (ABR)</div><div>--input_type contig</div><div>&nbsp;</div><div>bowtie2 (mapping)</div><div>--sensitive</div><div>&nbsp;</div><div>minimap2 (mapping)</div><div>-a</div><div>-x map-ont</div><div>&nbsp;</div><div>samtools mpileup (SNP&nbsp;detection)</div><div>-uRI</div><div>&nbsp;</div><div>bcftools call (SNP detection)</div><div>--variants-only</div><div>--skip-variants indels</div><div>--output-type v</div><div>--ploidy 1</div><div>-c</div><div>&nbsp;</div><div>SNPsift filter (SNP detection)</div><div>"( QUAL &gt;= 30 ) &amp; (( na FILTER ) | (FILTER = 'PASS')) &amp;</div><div>( DP &gt;= 20 ) &amp; ( MQ &gt;= 20 )"</div><div>&nbsp;</div><div>SNPeff ann (SNP detection)</div><div>-nodownload</div><div>-no-intron</div><div>-no-downstream</div><div>-no SPLICE_SITE_REGION</div><div>-upDownStreamLen 250</div><div>&nbsp;</div><div>bcftools consensus</div><div>(phylogenetic tree)</div><div>--haplotype 1</div><div>&nbsp;</div><div>fasttreemp</div><div>-nt</div><div>-boot 100</div><div>&nbsp;</div><div>roary</div><div>-e</div><div>-n</div><div>-cd 100</div><div>-g 100000</div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43268/kmer-a-suite-of-tools-for-dna-sequence-analysis</guid>
	<pubDate>Wed, 18 Aug 2021 00:02:54 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43268/kmer-a-suite-of-tools-for-dna-sequence-analysis</link>
	<title><![CDATA[Kmer: a suite of tools for DNA sequence analysis]]></title>
	<description><![CDATA[<p>More at&nbsp;https://help.rc.ufl.edu/doc/Kmer</p>
<p>This also includes:</p>
<ul>
<li>A2Amapper: ATAC, Assembly to Assembly Comparision tool:
<ul>
<li>Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).</li>
</ul>
</li>
</ul>
<ul>
<li>Sim4db:
<ul>
<li>Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.</li>
</ul>
</li>
</ul>
<ul>
<li>LEAFF:
<ul>
<li>LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.</li>
</ul>
</li>
</ul>
<ul>
<li>Meryl:
<ul>
<li>An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.</li>
</ul>
</li>
</ul><p>Address of the bookmark: <a href="https://help.rc.ufl.edu/doc/Kmer" rel="nofollow">https://help.rc.ufl.edu/doc/Kmer</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44288/upset-plots</guid>
	<pubDate>Fri, 24 Mar 2023 22:30:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44288/upset-plots</link>
	<title><![CDATA[Upset plots !]]></title>
	<description><![CDATA[<p>Upset plots are a type of visualization used to analyze the intersection of sets or categories. They are particularly useful for displaying data with multiple categories and analyzing their overlaps.</p>
<p>In an upset plot, each row represents a category or set, and each column represents a data point. The length of the bar for each category indicates the number of data points that belong to that category. The plot also shows the intersections between categories, represented by overlapping bars.</p>
<p>Upset plots are useful for visualizing complex data with multiple categories and intersections, and can help identify patterns and relationships between categories. They are often used in fields such as bioinformatics, where they can be used to analyze gene expression data or to compare the results of different experimental conditions.</p>
<p>https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions</p><p>Address of the bookmark: <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions" rel="nofollow">https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#example-with-the-genomic-regions</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44581/biokit-a-set-of-tools-dedicated-to-bioinformatics-data-visualisation</guid>
	<pubDate>Tue, 18 Jun 2024 02:04:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44581/biokit-a-set-of-tools-dedicated-to-bioinformatics-data-visualisation</link>
	<title><![CDATA[BioKit: a set of tools dedicated to bioinformatics, data visualisation]]></title>
	<description><![CDATA[<p><span>BioKit is a set of tools dedicated to bioinformatics, data visualisation (</span><a href="https://biokit.readthedocs.io/en/latest/references.html#module-biokit.viz" title="biokit.viz"><code><span>biokit.viz</span></code></a><span>), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis (e.g.,&nbsp;</span><a href="https://biokit.readthedocs.io/en/latest/references.html#module-biokit.stats" title="biokit.stats"><code><span>biokit.stats</span></code></a><span>). Since R is quite common in bioinformatics, we also provide a convenient module to run R inside your Python scripts or shell (:mod:biokit.rtools module).</span></p><p>Address of the bookmark: <a href="https://biokit.readthedocs.io/en/latest/index.html" rel="nofollow">https://biokit.readthedocs.io/en/latest/index.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/10409/check-linux-server-configuration</guid>
	<pubDate>Tue, 06 May 2014 01:10:57 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/10409/check-linux-server-configuration</link>
	<title><![CDATA[Check Linux server configuration !!]]></title>
	<description><![CDATA[<p>Bioinformatician uses servers for computational analysis. Sometime we need to check the server details before running our programs or tools. Here I am showing some basic commands using them you can gather the system/server information.<br /><br />To check what version of Operating System is installed on the server you can use the following commands:-<br />&nbsp;=================================================================<br />1.cat /etc/issue<br />[root@localhost ~]# cat /etc/issue<br />Red Hat Enterprise Linux Server release 5.5 (Tikanga)<br />Kernel \r on an \m<br /><br />2.cat /etc/redhat-release<br />[root@localhost ~]# cat /etc/redhat-release<br />Red Hat Enterprise Linux Server release 5.5 (Tikanga)<br /><br /><br />3.lsb_release -a<br />[root@localhost ~]# lsb_release -a<br />LSB Version:&nbsp;&nbsp;&nbsp; :core-3.1-ia32:core-3.1-noarch:graphics-3.1-ia32:graphics-3.1-noarch<br />Distributor ID: RedHatEnterpriseServer<br />Description:&nbsp;&nbsp;&nbsp; Red Hat Enterprise Linux Server release 5.5 (Tikanga)<br />Release:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5.5<br />Codename:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Tikanga<br /><br /><br /><br />To check whether the operating system is 32 or 64bit:-<br />================================<br /># uname -i<br />[root@localhost ~]# uname -i<br />i386<br />(i386 represents that server is having 32bit operating system)<br /><br />[root@localhost ~]# uname -i<br />x86_64<br />(x86_64 represents that server is having 64bit operating system)<br /><br />To see the processor/CPU information:-<br />=============================<br /># cat /proc/cpuinfo<br />[root@localhost ~] cat /proc/cpuinfo<br />processor&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 0<br />vendor_id&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : GenuineIntel<br />cpu family&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 6<br />model&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 15<br />model name&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : Intel(R) Xeon(R) CPU&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5130&nbsp; @ 2.00GHz<br />stepping&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 6<br />cpu MHz&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 1995.087<br />cache size&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 4096 KB<br />physical id&nbsp;&nbsp;&nbsp;&nbsp; : 0<br />siblings&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 2<br />core id&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 0<br />cpu cores&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 2<br />apicid&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 0<br />fdiv_bug&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : no<br />hlt_bug&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : no<br />f00f_bug&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : no<br />coma_bug&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : no<br />fpu&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : yes<br />fpu_exception&nbsp;&nbsp; : yes<br />cpuid level&nbsp;&nbsp;&nbsp;&nbsp; : 10<br />wp&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : yes<br />flags&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx lm constant_tsc pni monitor ds_cpl vmx tm2 ssse3 cx16 xtpr lahf_lm<br />bogomips&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; : 3990.17<br />(Here processor number 0 indicates that the system is having one process(processor number starts with zero))<br /><br /><br /><br /><br />To check memory information:-<br />===========================<br /># free -m<br />[root@localhost ~]# free -m<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; total&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; used&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; free&nbsp;&nbsp;&nbsp;&nbsp; shared&nbsp;&nbsp;&nbsp; buffers&nbsp;&nbsp;&nbsp;&nbsp; cached<br />Mem:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5066&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3513&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1552&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 612&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2319<br />-/+ buffers/cache:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 582&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4484<br />Swap:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1983&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1983<br /><br /><br /><br /># cat /proc/meminfo<br />[root@localhost ~]# cat /proc/meminfo<br />MemTotal:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5187752 kB<br />MemFree:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1639300 kB<br />Buffers:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 627024 kB<br />Cached:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2374944 kB<br />SwapCached:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 kB<br />Active:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2458788 kB<br />Inactive:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 920964 kB<br />HighTotal:&nbsp;&nbsp;&nbsp;&nbsp; 4325164 kB<br />HighFree:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1561936 kB<br />LowTotal:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 862588 kB<br />LowFree:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 77364 kB<br />SwapTotal:&nbsp;&nbsp;&nbsp;&nbsp; 2031608 kB<br />SwapFree:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2031608 kB<br />Dirty:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 704 kB<br />Writeback:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 kB<br />AnonPages:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 377892 kB<br />Mapped:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 35328 kB<br />Slab:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 153036 kB<br />PageTables:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 6316 kB<br />NFS_Unstable:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 kB<br />Bounce:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0 kB<br />CommitLimit:&nbsp;&nbsp; 4625484 kB<br />Committed_AS:&nbsp;&nbsp; 977132 kB<br />VmallocTotal:&nbsp;&nbsp; 116728 kB<br />VmallocUsed:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4492 kB<br />VmallocChunk:&nbsp;&nbsp; 112124 kB<br />HugePages_Total:&nbsp;&nbsp;&nbsp;&nbsp; 0<br />HugePages_Free:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0<br />HugePages_Rsvd:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0<br />Hugepagesize:&nbsp;&nbsp;&nbsp;&nbsp; 2048 kB<br /><br /><br />To check the model and serial name of the server:-<br />=======================================<br />[root@localhost ~]#&nbsp; dmidecode | egrep -i "product name|Serial number"<br />Product Name: PowerEdge R710<br />Serial Number: AB8CDE1<br />&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;<br /><br />To check the host name:-<br />=====================<br />[root@localhost ~]# uname -n<br />localhost<br /><br />[root@localhost ~]# hostname<br />localhost<br /><br />To check the kernel version:-<br />========================<br />[root@localhost ~]# uname -r<br />2.6.18-238.9.1.el5PAE</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/14868/bioinformaticians-summer-vacation</guid>
	<pubDate>Wed, 03 Sep 2014 13:11:50 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/14868/bioinformaticians-summer-vacation</link>
	<title><![CDATA[Bioinformatician&#039;s summer vacation !!!]]></title>
	<description><![CDATA[<p>Yes, the bioinformatician do spend their summer vacation like this. They spend more time on cheking the JOBS running on various servers.</p>]]></description>
	<dc:creator>Jit</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/14868" length="638462" type="image/png" />
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27238/slurm</guid>
	<pubDate>Wed, 04 May 2016 05:13:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27238/slurm</link>
	<title><![CDATA[SLURM]]></title>
	<description><![CDATA[<p><a href="http://www.schedmd.com/">SLURM</a> workload manager software, a free open-source workload manager designed specifically to satisfy the demanding needs of high performance computing.</p>
<p>This page is a <em>HOWTO</em> guide for setting up a <a href="http://www.schedmd.com/">SLURM</a> installation, currently focused on a CentOS 7 Linux OS. Please send feedback to Ole.H.Nielsen /at/ fysik.dtu.dk.</p>
<p>See the <a href="http://www.schedmd.com/">SLURM</a> homepage (also <a href="https://computing.llnl.gov/linux/slurm/">https://computing.llnl.gov/linux/slurm/</a>).</p><p>Address of the bookmark: <a href="https://wiki.fysik.dtu.dk/niflheim/SLURM" rel="nofollow">https://wiki.fysik.dtu.dk/niflheim/SLURM</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/43605/installing-elgg-on-ubuntu</guid>
	<pubDate>Thu, 25 Nov 2021 01:45:59 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/43605/installing-elgg-on-ubuntu</link>
	<title><![CDATA[Installing ELGG on Ubuntu !]]></title>
	<description><![CDATA[<p>Follow this:</p><h3>Settings file</h3><ul>
<li>
<div>
<div>
<div>Error</div>
<div>
<p>Your web server does not have permission to create the settings.php file in your installation directory. You have two choices:</p>
<p>1. Change the permissions on the elgg-config directory of your Elgg installation</p>
<p>2. Copy the file elgg-config/settings.example.php to elgg-config/settings.php and follow the instructions in it for setting your database parameters.</p>
</div>
</div>
</div>
</li>
</ul><p>&nbsp;</p><p>To resolve this --&nbsp;</p><p>Change the permision&nbsp;</p><p>chmod 777 elgg-config</p><h3>Web server</h3><ul>
<li>
<div>
<div>
<div>Warning</div>
<div>
<p>Your server does not support automatic testing of the rewrite rules and your browser does not support checking via JavaScript. You can continue the installation, but you may experience problems with your site. You can manually test the rewrite rules by clicking this link:&nbsp;test. You will see the word success if the rules are working.</p>
</div>
</div>
</div>
</li>
</ul><p>create a .httaccess</p><p>and provide detail in it</p><p><span style="text-decoration: underline;">Installation of Elgg</span><span></span></p><p>&nbsp;</p><p>(Note: Elgg requires&nbsp;<a href="http://www.cs.oswego.edu/~odendahl/misc/howto/mysql/">installing an instance of MySQL</a>.)</p><p>&nbsp;</p><p><span style="text-decoration: underline;">Steps to make adjustment and disposal of trial installations easier</span>.</p><p>&nbsp;</p><p><span style="text-decoration: underline;">MySQL</span></p><p>At this point, we assume you've set up your&nbsp;<tt>MySQL</tt>&nbsp;database</p><div><ol>
<li>Start your&nbsp;<tt>mysqld</tt>&nbsp;server daemon.<br />(For the sake of this example, we'll assume we're running on port 9999; you shouldn't actually use this port because only one daemon can run on any port number.)</li>
<li>Login to the server as&nbsp;<tt>root</tt>&nbsp;user, using the&nbsp;<tt>mysql</tt>&nbsp;client.</li>
<li>Create a database to store Elgg's tables. We'll call the database&nbsp;<tt>elggalpha</tt>.<br /><tt>mysql&gt; create database elggalpha;</tt></li>
<li>Grant access to a user &mdash; for this example we'll call him/her&nbsp;<tt>elggalphauser</tt>.
<pre>mysql&gt; grant all privileges on elggalpha.* to 'elggalphauser'@'moxie'
    -&gt; identified by 'secretpassword';
</pre>
</li>
</ol></div><p>&nbsp;</p><p><span style="text-decoration: underline;">Elgg</span></p><p>&nbsp;</p><div><ol>
<li>Type&nbsp;<tt>umask 022</tt></li>
<li>Change into your&nbsp;<tt>public_html</tt>&nbsp;directory (<em>aka</em>&nbsp;folder).<br /><tt>cd public_html</tt></li>
<li>make a directory called&nbsp;<tt>elgg</tt><br /><tt>mkdir elgg</tt></li>
<li>Change into the&nbsp;<tt>elgg</tt>&nbsp;subdirectory of&nbsp;<tt>public_html</tt>.<br /><tt>cd elgg</tt></li>
<li>download elgg into this directory</li>
<li>you'll end up with a file named<br /><tt>/home/<em>your-user-id</em>/public_html/elgg/elgg-X.X.X.X.zip</tt><br />(It's not literally&nbsp;<tt>X.X.X.X</tt>, it might be&nbsp;<tt>elgg-1.8.0.1.zip</tt>, for example.)</li>
<li>unzip elgg<br /><tt>unzip -q elgg-1.8.0.1.zip</tt></li>
<li>you'll end up with a directory (folder) named<br /><tt>/home/<em>your-user-id</em>/public_html/elgg/elgg-X.X.X.X</tt></li>
<li>make a symbolic link (<em>aka</em>&nbsp;shortcut) to this<br /><tt>ln -s elgg-X.X.X.X alpha</tt><br />(For example,&nbsp;<tt>ln -s elgg-1.8.0.1 alpha</tt>)</li>
<li>Give user&nbsp;<tt>nobody</tt>&nbsp;access to this directory<br /><tt>/usr/misc/bin/acl.sh -r -u nobody elgg-1.8.0.1</tt></li>
<li>create a data directory for&nbsp;<tt>elgg</tt>&nbsp;(get into your home directory first):
<pre>cd
mkdir -p elgg/alpha/data
chmod -R 755 elgg/alpha/data
</pre>
</li>
<li>Change into the&nbsp;<tt>elgg/alpha</tt>&nbsp;directory.<br /><tt>cd elgg/alpha</tt></li>
<li>Give user&nbsp;<tt>nobody</tt>&nbsp;access to this subdirectory&nbsp;<tt>data</tt><br /><tt>/usr/misc/bin/acl.sh -u nobody data</tt></li>
<li>In your browser, navigate to your elgg installation<br /><tt>http://moxie.cs.oswego.edu/~<em>your-user-id</em>/elgg/alpha/</tt><br />You'll have a screen which includes this message:
<pre>Welcome

Installing Elgg has 6 simple steps and reading this welcome is the first one!

If you haven't already, read through the installation instructions included with Elgg (or click the instructions link at the bottom of the page).

If you are ready to proceed, click the Next button.
</pre>
</li>
<li>Follow configuration process:
<ul>
<li>The first screen probably will contain a success message in green and a failure message in pink:
<pre><span>Requirements check</span>

Your server failed the requirements check. After you have fixed the below issues, refresh this
page. Check the troubleshooting links at the bottom of this page if you need further assistance.
<span>PHP</span></pre>
<div>Your server's PHP satisfies all of Elgg's requirements.</div>
<pre>
<span>Web server</span></pre>
<div>We think your server is running the Apache web server. The rewrite test failed and the most likely cause is that AllowOverride is not set to All for Elgg's directory. This prevents Apache from processing the .htaccess file which contains the rewrite rules. A less likely cause is Apache is configured with an alias for your Elgg directory and you need to set the RewriteBase in your .htaccess. There are further instructions in the .htaccess file in your Elgg directory.</div>
<pre>
<span>Database</span></pre>
<div>The database requirements are checked when Elgg loads its database.</div>
</li>
<li>To correct this, replace the&nbsp;<tt>.htaccess</tt>&nbsp;file that Elgg created with one that you can edit:
<pre>cp -ip .htaccess temp-htaccess
rm .htaccess
mv temp-htaccess .htaccess
</pre>
</li>
<li>Edit the&nbsp;<tt>.htaccess</tt>&nbsp;file: Go to approximately line 101 (where it says&nbsp;<tt>#RewriteBase /</tt>) and add the line:<br /><tt>RewriteBase /~<em>your-user-id</em>/elgg/alpha/</tt></li>
<li>Be sure to save the edited file.
<p>&nbsp;</p>
<p>&nbsp;</p>
</li>
<li>Click the&nbsp;<span>Refresh</span>&nbsp;button.
<p>&nbsp;</p>
<p>&nbsp;</p>
</li>
<li>If this hasn't fixed things, seek professional help.
<p>&nbsp;</p>
<p>&nbsp;</p>
</li>
<li>Click the&nbsp;<span>Next</span>&nbsp;button.
<p>&nbsp;</p>
<p>&nbsp;</p>
</li>
<li>Fill in the parameters appropriate to your MySQL installation.
<pre><span>Database installation</span>

If you haven't already created a database for Elgg, do that now. Then fill in the values below to
initialize the Elgg database.

<span>Database Username</span></pre>
<div>elggalphauser</div>
<pre>User that has full priviledges to the MySQL database that you created for Elgg

<span>Database Password</span></pre>
<div>secretpassword</div>
<pre>Password for the above database user account

<span>Database Name</span></pre>
<div>elggalpha</div>
<pre>Name of the Elgg database

<span>Database Host</span></pre><sup>&Dagger;</sup>
<div>moxie:9999</div>
<pre>Hostname of the MySQL server (usually localhost)
<strong>&Dagger;You might need to use <tt>127.0.0.1:9999</tt> for the host
    if you haven't set up MySQL as we've done.</strong>



<span>Database Table Prefix</span></pre>
<div>elgg_</div>
<pre>The prefix given to all of Elgg's tables (usually elgg_)
</pre>
<div><span>Next</span></div>
<p>&nbsp;</p>
<p>&nbsp;</p>
</li>
<li>Continue filling in forms as requested.
<pre>Configure site</pre>
<div>Database has been installed.</div>
<pre>
We need some information about the site as we configure Elgg. If you haven't created a data directory for Elgg, you need to do so now.

<span>Site Name</span></pre>
<div>My Elgg Site version Alpha</div>
<pre>The name of your new Elgg site

<span>Site Email Address</span></pre>
<div><em>your-user-id</em>@oswego.edu</div>
<pre>Email address used by Elgg for communication with users

<span>Site URL</span></pre>
<div>http://moxie.cs.oswego.edu/~<em>your-user-id</em>/elgg/alpha/</div>
<pre>The address of the site (Elgg usually guesses this correctly)

<span>Elgg Install Directory</span></pre>
<div>/home/<em>your-user-id</em>/public_html/elgg/elgg.1.8.0.1/</div>
<pre>The directory where you put the Elgg code (Elgg usually guesses this correctly)

<span>Data Directory</span></pre>
<div>/home/<em>your-user-id</em>/elgg/alpha/data</div>
<pre>The directory that you created for Elgg to save files (the permissions on this directory are checked
when you click Next)

<span>Default Site Access</span></pre>
<div>Public</div>
<pre>The default access level for new user created content
</pre>
</li>
<li>
<pre><span>Create admin account</span></pre>
<div>Site settings have been saved.</div>
<pre>
It is now time to create an administrator's account.

<span>Display Name</span></pre>
<div>&nbsp;</div>
<pre>The name that is displayed on the site for this account

<span>Email Address</span></pre>
<div>&nbsp;</div>
<pre>
<span>Username</span></pre>
<div>&nbsp;</div>
<pre>Account username used for logging in

<span>Password</span></pre>
<div>&nbsp;</div>
<pre>Account password must be at least 6 characters long

<span>Password Again</span></pre>
<div>&nbsp;</div>
<pre>Retype password to confirm</pre>
</li>
</ul>
</li>
</ol></div>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

</channel>
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