<?xml version="1.0" encoding="UTF-8"?><rss
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> <channel><title>Comments for Autarchy of the Private Cave</title> <atom:link href="https://bogdan.org.ua/comments/feed" rel="self" type="application/rss+xml" /><link>https://bogdan.org.ua</link> <description>Tiny bits of bioinformatics, [web-]programming etc</description> <lastBuildDate>Mon, 01 Jan 2024 17:12:20 +0000</lastBuildDate> <sy:updatePeriod>hourly</sy:updatePeriod> <sy:updateFrequency>1</sy:updateFrequency> <generator>https://wordpress.org/?v=3.8.27</generator> <item><title>Comment on How to: convert your VPS root filesystem to btrfs (using rescue boot) by Tacco</title><link>https://bogdan.org.ua/2016/02/15/how-to-convert-your-vps-root-filesystem-to-btrfs-using-rescue-boot.html#comment-754834</link> <dc:creator><![CDATA[Tacco]]></dc:creator> <pubDate>Mon, 01 Jan 2024 17:12:20 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=2349#comment-754834</guid> <description><![CDATA[Great tutorial. But for those wanting to replicate an environment in which you want to use Timeshift to take snapshots, i would recommend to follow the tutorial made by Howtoforge (the one in you mentioned). For those having a boot partition (ext4 in my case), don&#039;t forget to mount that partition as well once you run the grub update/install. Thank you very much for your effort.]]></description> <content:encoded><![CDATA[<p>Great tutorial. But for those wanting to replicate an environment in which you want to use Timeshift to take snapshots, i would recommend to follow the tutorial made by Howtoforge (the one in you mentioned). For those having a boot partition (ext4 in my case), don&#8217;t forget to mount that partition as well once you run the grub update/install. Thank you very much for your effort.</p> ]]></content:encoded> </item> <item><title>Comment on How to truncate git history (sample script included) by JT</title><link>https://bogdan.org.ua/2011/03/28/how-to-truncate-git-history-sample-script-included.html#comment-749853</link> <dc:creator><![CDATA[JT]]></dc:creator> <pubDate>Mon, 29 Mar 2021 15:50:54 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=1481#comment-749853</guid> <description><![CDATA[This works, but you will loose all timestamps for commits that are retained.  Seems like the git team should address a real need to perform housekeeping for repos that undergo lots of change over many years.]]></description> <content:encoded><![CDATA[<p>This works, but you will loose all timestamps for commits that are retained.  Seems like the git team should address a real need to perform housekeeping for repos that undergo lots of change over many years.</p> ]]></content:encoded> </item> <item><title>Comment on How to fix: Xiaomi Mi Band stopped tracking steps and sleep by Charlotte Semaan</title><link>https://bogdan.org.ua/2015/07/26/how-to-fix-xiaomi-mi-band-stopped-tracking-steps-and-sleep.html#comment-735679</link> <dc:creator><![CDATA[Charlotte Semaan]]></dc:creator> <pubDate>Wed, 18 Mar 2020 07:38:43 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=2301#comment-735679</guid> <description><![CDATA[it worked for me today for a mi fit band version 1 paired on a Xiaomi Mi A2 Lite phone, Android 9 software, and mi fit app version 4.0.15..
my band wasn&#039;t monitoring my steps and sleep it&#039;s been around 2 weeks even though it&#039;s charged and paired..
thank youuuuuu..]]></description> <content:encoded><![CDATA[<p>it worked for me today for a mi fit band version 1 paired on a Xiaomi Mi A2 Lite phone, Android 9 software, and mi fit app version 4.0.15..<br
/> my band wasn&#8217;t monitoring my steps and sleep it&#8217;s been around 2 weeks even though it&#8217;s charged and paired..<br
/> thank youuuuuu..</p> ]]></content:encoded> </item> <item><title>Comment on How to fix: Xiaomi Mi Band stopped tracking steps and sleep by SAM</title><link>https://bogdan.org.ua/2015/07/26/how-to-fix-xiaomi-mi-band-stopped-tracking-steps-and-sleep.html#comment-727745</link> <dc:creator><![CDATA[SAM]]></dc:creator> <pubDate>Thu, 13 Jun 2019 14:15:55 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=2301#comment-727745</guid> <description><![CDATA[Hi,
I have Mi Band 2 with Mi Fit 4.0.0 it was working fine until last week were it was stuck in 0 steps and it is not tracking sleep anymore
heart pulse is working fine and time can also be synchronized without problem.
I&#039;ve tried your solution and i&#039;ve found that the band was on do not disturb mode and now it accepts and vibrates when incoming calls but still not counting steps :(
does anyone have solved this issue ?]]></description> <content:encoded><![CDATA[<p>Hi,</p><p>I have Mi Band 2 with Mi Fit 4.0.0 it was working fine until last week were it was stuck in 0 steps and it is not tracking sleep anymore</p><p>heart pulse is working fine and time can also be synchronized without problem.</p><p>I&#8217;ve tried your solution and i&#8217;ve found that the band was on do not disturb mode and now it accepts and vibrates when incoming calls but still not counting steps <img
src="https://bogdan.org.ua/wp-includes/images/smilies/icon_sad.gif" alt=":(" class="wp-smiley" /></p><p>does anyone have solved this issue ?</p> ]]></content:encoded> </item> <item><title>Comment on Convert MySQL database from one encoding/collation into another by SY</title><link>https://bogdan.org.ua/2008/02/08/convert-mysql-database-from-one-encodingcollation-into-another.html#comment-724244</link> <dc:creator><![CDATA[SY]]></dc:creator> <pubDate>Thu, 09 May 2019 18:40:34 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/2008/02/08/convert-mysql-database-from-one-encodingcollation-into-another.html#comment-724244</guid> <description><![CDATA[Updated for mysqli:
&lt;code&gt;
query(&quot; SHOW TABLES &quot;) or die($mysqli-&gt;error);
while ($row_tables = $rs_tables-&gt;fetch_row()) {
$table = $mysqli-&gt;real_escape_string($row_tables[0]);
// Alter table collation
// ALTER TABLE `account` DEFAULT CHARACTER SET utf8
if ($show_alter_table)
echo(&quot;ALTER TABLE `$table` DEFAULT CHARACTER SET $character_set;\n&quot;);
$rs = $mysqli-&gt;query(&quot; SHOW FULL FIELDS FROM `$table` &quot;) or die($mysqli-&gt;error);
while ($row = $rs-&gt;fetch_assoc()) {
if ($row[&#039;Collation&#039;] == &#039;&#039; &#124;&#124; $row[&#039;Collation&#039;] == $convert_to)
continue;
// Is the field allowed to be null?
if ($row[&#039;Null&#039;] == &#039;YES&#039;)
$nullable = &#039; NULL &#039;;
else
$nullable = &#039; NOT NULL &#039;;
// Does the field default to null, a string, or nothing?
if ($row[&#039;Default&#039;] === null &amp;&amp; $row[&#039;Null&#039;] == &#039;YES&#039;)
$default = &quot; DEFAULT NULL &quot;;
elseif ($row[&#039;Default&#039;] != &#039;&#039;)
$default = &quot; DEFAULT &#039;&quot; . $mysqli-&gt;real_escape_string($row[&#039;Default&#039;]) . &quot;&#039;&quot;;
else
$default = &#039;&#039;;
// sanity check and fix:
if ($nullable == &#039; NOT NULL &#039; &amp;&amp; $default == &#039; DEFAULT NULL &#039;) {
$default = &#039;&#039;;
echo &quot;/* Warning: wrong combination of &#039;default value&#039; and &#039;NULL-flag&#039; detected - and fixed! */\n&quot;;
echo &quot;/* Diagnostics: row[Null] = &#039;$row[Null]&#039;, row[Default] = &quot; . $mysqli-&gt;real_escape_string($row[&#039;Default&#039;]) . &quot;, MySQL version: &quot; . $mysqli-&gt;get_server_info() . &quot; */\n&quot;;
}
// Don&#039;t alter INT columns: no collations, and altering them drops autoincrement values
if (strpos($row[&#039;Type&#039;], &#039;int&#039;) !== false) {
$show_alter_field = false;
} else {
$show_alter_field = true;
}
// Alter field collation:
// ALTER TABLE `tab` CHANGE `field` `field` CHAR( 5 ) CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL
if ($show_alter_field) {
$field = $mysqli-&gt;real_escape_string($row[&#039;Field&#039;]);
echo &quot;ALTER TABLE `$table` CHANGE `$field` `$field` $row[Type] CHARACTER SET $character_set COLLATE $convert_to $nullable $default;\n&quot;;
}
}
}
&lt;/code&gt;]]></description> <content:encoded><![CDATA[<p>Updated for mysqli:</p><p><code><br
/> query(" SHOW TABLES ") or die($mysqli-&gt;error);</p><p>while ($row_tables = $rs_tables-&gt;fetch_row()) {<br
/> $table = $mysqli-&gt;real_escape_string($row_tables[0]);</p><p> // Alter table collation<br
/> // ALTER TABLE `account` DEFAULT CHARACTER SET utf8<br
/> if ($show_alter_table)<br
/> echo("ALTER TABLE `$table` DEFAULT CHARACTER SET $character_set;\n");</p><p> $rs = $mysqli-&gt;query(" SHOW FULL FIELDS FROM `$table` ") or die($mysqli-&gt;error);</p><p> while ($row = $rs-&gt;fetch_assoc()) {</p><p> if ($row['Collation'] == '' || $row['Collation'] == $convert_to)<br
/> continue;</p><p> // Is the field allowed to be null?<br
/> if ($row['Null'] == 'YES')<br
/> $nullable = ' NULL ';<br
/> else<br
/> $nullable = ' NOT NULL ';</p><p> // Does the field default to null, a string, or nothing?<br
/> if ($row['Default'] === null &amp;&amp; $row['Null'] == 'YES')<br
/> $default = " DEFAULT NULL ";<br
/> elseif ($row['Default'] != '')<br
/> $default = " DEFAULT '" . $mysqli-&gt;real_escape_string($row['Default']) . "'";<br
/> else<br
/> $default = '';</p><p> // sanity check and fix:<br
/> if ($nullable == ' NOT NULL ' &amp;&amp; $default == ' DEFAULT NULL ') {<br
/> $default = '';<br
/> echo "/* Warning: wrong combination of 'default value' and 'NULL-flag' detected - and fixed! */\n";<br
/> echo "/* Diagnostics: row[Null] = '$row[Null]', row[Default] = " . $mysqli-&gt;real_escape_string($row['Default']) . ", MySQL version: " . $mysqli-&gt;get_server_info() . " */\n";<br
/> }</p><p> // Don't alter INT columns: no collations, and altering them drops autoincrement values<br
/> if (strpos($row['Type'], 'int') !== false) {<br
/> $show_alter_field = false;<br
/> } else {<br
/> $show_alter_field = true;<br
/> }</p><p> // Alter field collation:<br
/> // ALTER TABLE `tab` CHANGE `field` `field` CHAR( 5 ) CHARACTER SET utf8 COLLATE utf8_general_ci NULL DEFAULT NULL<br
/> if ($show_alter_field) {<br
/> $field = $mysqli-&gt;real_escape_string($row['Field']);<br
/> echo "ALTER TABLE `$table` CHANGE `$field` `$field` $row[Type] CHARACTER SET $character_set COLLATE $convert_to $nullable $default;\n";<br
/> }<br
/> }<br
/> }<br
/> </code></p> ]]></content:encoded> </item> <item><title>Comment on Citation and reference managers for Linux: short overview by Bogdan</title><link>https://bogdan.org.ua/2008/10/29/citation-and-reference-managers-for-linux-short-overview.html#comment-595098</link> <dc:creator><![CDATA[Bogdan]]></dc:creator> <pubDate>Thu, 14 Jun 2018 18:51:44 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=430#comment-595098</guid> <description><![CDATA[@Klaus, papis looks nice - command line, yay! Alas, I seem to no longer have any need in citation/reference managers...]]></description> <content:encoded><![CDATA[<p>@Klaus, papis looks nice &#8211; command line, yay! Alas, I seem to no longer have any need in citation/reference managers&#8230;</p> ]]></content:encoded> </item> <item><title>Comment on Citation and reference managers for Linux: short overview by Klaus</title><link>https://bogdan.org.ua/2008/10/29/citation-and-reference-managers-for-linux-short-overview.html#comment-588818</link> <dc:creator><![CDATA[Klaus]]></dc:creator> <pubDate>Tue, 29 May 2018 14:23:54 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=430#comment-588818</guid> <description><![CDATA[What about papis? https://github.com/papis/papis ?]]></description> <content:encoded><![CDATA[<p>What about papis? <a
href="https://github.com/papis/papis" rel="nofollow">https://github.com/papis/papis</a> ?</p> ]]></content:encoded> </item> <item><title>Comment on Mail-in-a-box, Sovereign, Modoboa, iRedMail, etc by Bogdan</title><link>https://bogdan.org.ua/2016/12/28/mail-in-a-box-sovereign-modoboa-iredmail-etc.html#comment-587969</link> <dc:creator><![CDATA[Bogdan]]></dc:creator> <pubDate>Sun, 27 May 2018 19:33:26 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=2465#comment-587969</guid> <description><![CDATA[Andre, thank you for the link! Homebox does look interesting; I&#039;ll check it out in more details next time when I need to set up a mail server :)]]></description> <content:encoded><![CDATA[<p>Andre, thank you for the link! Homebox does look interesting; I&#8217;ll check it out in more details next time when I need to set up a mail server <img
src="https://bogdan.org.ua/wp-includes/images/smilies/icon_smile.gif" alt=":)" class="wp-smiley" /></p> ]]></content:encoded> </item> <item><title>Comment on Mail-in-a-box, Sovereign, Modoboa, iRedMail, etc by Andre Rodier</title><link>https://bogdan.org.ua/2016/12/28/mail-in-a-box-sovereign-modoboa-iredmail-etc.html#comment-587929</link> <dc:creator><![CDATA[Andre Rodier]]></dc:creator> <pubDate>Sun, 27 May 2018 17:44:34 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=2465#comment-587929</guid> <description><![CDATA[Well, you may now add another one to the list.
The good points: protection against physical intrusion using LUKS (optional) and remote intrusion (AppArmor)
Using Debian repository only (no git clone / wget / curl / etc.)
Single sign-on via LDAP.
For the packages, the minimum required to send emails for now, but does it well.
The last version came with a Jabber server.
http://homebox.readthedocs.io/en/latest/
Enjoy!]]></description> <content:encoded><![CDATA[<p>Well, you may now add another one to the list.</p><p>The good points: protection against physical intrusion using LUKS (optional) and remote intrusion (AppArmor)<br
/> Using Debian repository only (no git clone / wget / curl / etc.)<br
/> Single sign-on via LDAP.<br
/> For the packages, the minimum required to send emails for now, but does it well.<br
/> The last version came with a Jabber server.</p><p><a
href="http://homebox.readthedocs.io/en/latest/" rel="nofollow">http://homebox.readthedocs.io/en/latest/</a></p><p>Enjoy!</p> ]]></content:encoded> </item> <item><title>Comment on How to fix &#8220;MySQL server has gone away&#8221; (error 2006) by Angbuhang</title><link>https://bogdan.org.ua/2008/12/25/how-to-fix-mysql-server-has-gone-away-error-2006.html#comment-573367</link> <dc:creator><![CDATA[Angbuhang]]></dc:creator> <pubDate>Wed, 25 Apr 2018 06:31:21 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=464#comment-573367</guid> <description><![CDATA[Thanks !! It really worked out error has gone.]]></description> <content:encoded><![CDATA[<p>Thanks !! It really worked out error has gone.</p> ]]></content:encoded> </item> <item><title>Comment on How to fix &#8220;MySQL server has gone away&#8221; (error 2006) by Blackjuker</title><link>https://bogdan.org.ua/2008/12/25/how-to-fix-mysql-server-has-gone-away-error-2006.html#comment-564575</link> <dc:creator><![CDATA[Blackjuker]]></dc:creator> <pubDate>Wed, 28 Mar 2018 04:35:09 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=464#comment-564575</guid> <description><![CDATA[When configuring the Machine Data Source for the ODBC connection, the MySQL Connector/ODBC GUI opens. By expanding the â€œDetailsâ€, selecting tab â€œFlag 1â€ and checking the â€œEnable automatic reconnectâ€ option, the â€œMySQL server has gone away (error 2006)â€ problem was eliminated.]]></description> <content:encoded><![CDATA[<p>When configuring the Machine Data Source for the ODBC connection, the MySQL Connector/ODBC GUI opens. By expanding the â€œDetailsâ€, selecting tab â€œFlag 1â€ and checking the â€œEnable automatic reconnectâ€ option, the â€œMySQL server has gone away (error 2006)â€ problem was eliminated.</p> ]]></content:encoded> </item> <item><title>Comment on How to fix: Xiaomi Mi Band stopped tracking steps and sleep by Gondor</title><link>https://bogdan.org.ua/2015/07/26/how-to-fix-xiaomi-mi-band-stopped-tracking-steps-and-sleep.html#comment-544319</link> <dc:creator><![CDATA[Gondor]]></dc:creator> <pubDate>Fri, 12 Jan 2018 17:30:59 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=2301#comment-544319</guid> <description><![CDATA[Thanks! Worked to me and my problem (stop counting steps)
Thank you!]]></description> <content:encoded><![CDATA[<p>Thanks! Worked to me and my problem (stop counting steps)</p><p>Thank you!</p> ]]></content:encoded> </item> <item><title>Comment on Executing and checking background shell process from PHP by daianne</title><link>https://bogdan.org.ua/2007/05/23/executing-and-checking-background-shell-process-from-php.html#comment-541378</link> <dc:creator><![CDATA[daianne]]></dc:creator> <pubDate>Wed, 20 Dec 2017 09:09:36 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/2007/05/23/executing-and-checking-background-shell-process-from-php.html#comment-541378</guid> <description><![CDATA[@Bogdan,
Thank you very much for your response and advice. I already did that, but so far the only one that works for me is to write the message on a file. However, i don&#039;t know how should i detect the error on that file, because if i&#039;m going to search the word &#039;Error or &#039;Failed&#039;, it will take forever since my data testing is more than 30gb. And i can&#039;t get to work out the thing that you said to check the file size since the log also writes the process on the file created. So even if I check the file size, it wont help me because it will always be greater than zero.
as for the alternative that you mention I can&#039;t get the exit code. Or better yet I&#039;m not sure how to get it done.]]></description> <content:encoded><![CDATA[<p>@Bogdan,<br
/> Thank you very much for your response and advice. I already did that, but so far the only one that works for me is to write the message on a file. However, i don&#8217;t know how should i detect the error on that file, because if i&#8217;m going to search the word &#8216;Error or &#8216;Failed&#8217;, it will take forever since my data testing is more than 30gb. And i can&#8217;t get to work out the thing that you said to check the file size since the log also writes the process on the file created. So even if I check the file size, it wont help me because it will always be greater than zero.</p><p>as for the alternative that you mention I can&#8217;t get the exit code. Or better yet I&#8217;m not sure how to get it done.</p> ]]></content:encoded> </item> <item><title>Comment on Executing and checking background shell process from PHP by Bogdan</title><link>https://bogdan.org.ua/2007/05/23/executing-and-checking-background-shell-process-from-php.html#comment-541185</link> <dc:creator><![CDATA[Bogdan]]></dc:creator> <pubDate>Mon, 18 Dec 2017 20:25:53 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/2007/05/23/executing-and-checking-background-shell-process-from-php.html#comment-541185</guid> <description><![CDATA[@Daianne,
one of the ways would be to redirect stdout and stderr to files, and then check those files for any messages about success or failure - or even check if stdout/stderr/output files are larger than zero bytes (because zero may indicate an early failure, if the process is not running anymore).
Alternatively/in addition, if you start a shell script wrapper around your target application, then you can collect (from the shell script) the exit code of your target application and write it to some file, and then check if exit code was 0 or not.]]></description> <content:encoded><![CDATA[<p>@Daianne,<br
/> one of the ways would be to redirect stdout and stderr to files, and then check those files for any messages about success or failure &#8211; or even check if stdout/stderr/output files are larger than zero bytes (because zero may indicate an early failure, if the process is not running anymore).</p><p>Alternatively/in addition, if you start a shell script wrapper around your target application, then you can collect (from the shell script) the exit code of your target application and write it to some file, and then check if exit code was 0 or not.</p> ]]></content:encoded> </item> <item><title>Comment on Executing and checking background shell process from PHP by daianne</title><link>https://bogdan.org.ua/2007/05/23/executing-and-checking-background-shell-process-from-php.html#comment-541119</link> <dc:creator><![CDATA[daianne]]></dc:creator> <pubDate>Mon, 18 Dec 2017 06:57:06 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/2007/05/23/executing-and-checking-background-shell-process-from-php.html#comment-541119</guid> <description><![CDATA[Hi, using this how would i catch the error if the command i execute has failed?]]></description> <content:encoded><![CDATA[<p>Hi, using this how would i catch the error if the command i execute has failed?</p> ]]></content:encoded> </item> <item><title>Comment on How to fix: Xiaomi Mi Band stopped tracking steps and sleep by Jaquline</title><link>https://bogdan.org.ua/2015/07/26/how-to-fix-xiaomi-mi-band-stopped-tracking-steps-and-sleep.html#comment-536022</link> <dc:creator><![CDATA[Jaquline]]></dc:creator> <pubDate>Wed, 15 Nov 2017 07:27:07 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=2301#comment-536022</guid> <description><![CDATA[Thanks a ton, This worked for me as well. That was soo rediculus to enable phone call and the make a call from another number then it started working :)
Thank you,
J]]></description> <content:encoded><![CDATA[<p>Thanks a ton, This worked for me as well. That was soo rediculus to enable phone call and the make a call from another number then it started working <img
src="https://bogdan.org.ua/wp-includes/images/smilies/icon_smile.gif" alt=":)" class="wp-smiley" /></p><p>Thank you,<br
/> J</p> ]]></content:encoded> </item> <item><title>Comment on Practical comparison of NGS adapter trimming tools by Bogdan</title><link>https://bogdan.org.ua/2016/06/01/practical-comparison-of-ngs-adapter-trimming-tools.html#comment-527317</link> <dc:creator><![CDATA[Bogdan]]></dc:creator> <pubDate>Thu, 14 Sep 2017 20:43:19 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=2428#comment-527317</guid> <description><![CDATA[Hi Brian,
thank you for stopping by and offering a fix! I wonder how you found this page :)
As you probably noticed, this is not a proper comparison with any degree of rigor - but rather a quick pick of &quot;whatever seems to work&quot;.
This is why I have not invested much effort into making BBduk run...
I&#039;m definitely still interested in using the entire BBMAP suite - the comparison plots on sourceforge page are quite attractive.
As I&#039;m still working with all kinds of NGS data, I&#039;ll give BBMAP a proper try in one of my next projects.]]></description> <content:encoded><![CDATA[<p>Hi Brian,</p><p>thank you for stopping by and offering a fix! I wonder how you found this page <img
src="https://bogdan.org.ua/wp-includes/images/smilies/icon_smile.gif" alt=":)" class="wp-smiley" /></p><p>As you probably noticed, this is not a proper comparison with any degree of rigor &#8211; but rather a quick pick of &#8220;whatever seems to work&#8221;.<br
/> This is why I have not invested much effort into making BBduk run&#8230;</p><p>I&#8217;m definitely still interested in using the entire BBMAP suite &#8211; the comparison plots on sourceforge page are quite attractive.</p><p>As I&#8217;m still working with all kinds of NGS data, I&#8217;ll give BBMAP a proper try in one of my next projects.</p> ]]></content:encoded> </item> <item><title>Comment on Practical comparison of NGS adapter trimming tools by Brian Bushnell</title><link>https://bogdan.org.ua/2016/06/01/practical-comparison-of-ngs-adapter-trimming-tools.html#comment-523913</link> <dc:creator><![CDATA[Brian Bushnell]]></dc:creator> <pubDate>Thu, 07 Sep 2017 05:19:02 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=2428#comment-523913</guid> <description><![CDATA[Hi!
I&#039;m not really sure why BBDuk did not work for you, but you can try this -
At the bottom of bbduk.sh is this line:
local CMD=&quot;java -Djava.library.path=$NATIVELIBDIR $EA $z $z2 -cp $CP jgi.BBDukF $@&quot;
Change that to:
local CMD=&quot;java $EA $z $z2 -cp $CP jgi.BBDukF $@&quot;
...and then it should not encounter any JNI-related problems.]]></description> <content:encoded><![CDATA[<p>Hi!</p><p>I&#8217;m not really sure why BBDuk did not work for you, but you can try this &#8211;</p><p>At the bottom of bbduk.sh is this line:<br
/> local CMD=&#8221;java -Djava.library.path=$NATIVELIBDIR $EA $z $z2 -cp $CP jgi.BBDukF $@&#8221;</p><p>Change that to:<br
/> local CMD=&#8221;java $EA $z $z2 -cp $CP jgi.BBDukF $@&#8221;</p><p>&#8230;and then it should not encounter any JNI-related problems.</p> ]]></content:encoded> </item> <item><title>Comment on Practical comparison of NGS adapter trimming tools by Bogdan</title><link>https://bogdan.org.ua/2016/06/01/practical-comparison-of-ngs-adapter-trimming-tools.html#comment-522028</link> <dc:creator><![CDATA[Bogdan]]></dc:creator> <pubDate>Tue, 29 Aug 2017 19:48:08 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=2428#comment-522028</guid> <description><![CDATA[Hi Joyce, I haven&#039;t added any custom adapters to the file provided with Trimmomatic, so I don&#039;t remember the naming conventions - but they are described in the Trimmomatic manual.]]></description> <content:encoded><![CDATA[<p>Hi Joyce, I haven&#8217;t added any custom adapters to the file provided with Trimmomatic, so I don&#8217;t remember the naming conventions &#8211; but they are described in the Trimmomatic manual.</p> ]]></content:encoded> </item> <item><title>Comment on Practical comparison of NGS adapter trimming tools by Joyce</title><link>https://bogdan.org.ua/2016/06/01/practical-comparison-of-ngs-adapter-trimming-tools.html#comment-520864</link> <dc:creator><![CDATA[Joyce]]></dc:creator> <pubDate>Tue, 22 Aug 2017 08:17:38 +0000</pubDate> <guid
isPermaLink="false">http://bogdan.org.ua/?p=2428#comment-520864</guid> <description><![CDATA[Hi,
I&#039;m new to using trimmomatic. Been trying to get it to remove adapter sequences but it keeps missing out on the ones I specified in my adapter fasts file. Can you share with me the naming conventions needed for the trimmer to work?
Thanks!]]></description> <content:encoded><![CDATA[<p>Hi,<br
/> I&#8217;m new to using trimmomatic. Been trying to get it to remove adapter sequences but it keeps missing out on the ones I specified in my adapter fasts file. Can you share with me the naming conventions needed for the trimmer to work?</p><p>Thanks!</p> ]]></content:encoded> </item> </channel> </rss>