I am new to Bowtie. I am trying to use Bowtie for end to end local alignment. I've got this error message:
Could not locate a Bowtie index corresponding to basename "/bowtie2-index/hg19"
In my installation and in the bowtie2-index/hg19 folder there are six bt2 files. I am using the following command:
/opt/bowtie2/bowtie2-align-s --wrapper basic-0 -p 64 -x /mnt/miczfs/tide/bowtie2-index/hg19 -S /mnt/miczfs/tide/Data/chr2chr3/chr2chr3.sam -1 /mnt/miczfs/tide/Data/chr2chr3/chr2chr3.f1.fastq -2 /mnt/miczfs/tide/Data/chr2chr3/chr2chr3.f2.fastq
This is a perennial question, I guess the documentation isn't explicit enough here. By using -x /mnt/miczfs/tide/bowtie2-index/hg19, you're telling bowtie2 that you have files like /mnt/miczfs/tide/bowtie2-index/hg19.1.bt2 that it should use. You don't specify a folder, you specify a "basename". You probably meant -x /mnt/miczfs/tide/bowtie2-index/hg19/hg19 or something like that.
Related
I am on Qubes OS. That means fedora-25 as dom0. I would like to change the configs for "notification area" alias "systray" plugin of xfce. How can I do it. I would like to delete/add one item.
The Gui only gives me the option to hide with ugly arrow on the side or to "clear all known applications". However, regarding the last option I am afraid to lose the notification area as it is and never get it back.
I looked with the "find" command for "xfce4" and "xfce4-plugins" and so on. All the files I could find, e.g. in ~/.config/xfce4, could not help me. I can nowhere find a config file for the plugin.
Thanks in advance :)
Known applications is stored as an array in xfconf, in the xfce4-panel channel and under the property /plugins/plugin-[id]/known-items, where the plugin id is dynamic and depends on the order plugins were added to panel.
You could hack your way messing with ~/.config/xfce4/xfconf/xfce-perchannel-xml/xfce4-panel.xml but I strongly advise you not to, instead use xfconf-query to read and set values.
I'm going to write down some snippets below so you can use them to craft a script that suits your needs:
# Find the plugin id, can be empty if systray is not present
xfconf-query -c xfce4-panel -p /plugins -l -v | grep systray | grep -Po "plugin-\\d+" | head -n1
# Get array of current known apps
xfconf-query -c xfce4-panel -p /plugins/$PLUGIN_ID/known-items | tail -n +3
# Set array of known apps
xfconf-query -c xfce4-panel -p /plugins/$PLUGIN_ID/known-items -t string -s value1 -t string -s value2 ...
I'm running the command -ascp -v -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh -k 1 -T -l200m anonftp#ftp-private.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR590/SRR5907429 /SRR5907429 .sra ~/sra_download with Linux
and I get this error -
"user#host:" in all sources must match
What does this mean?How to solve it?
First,"-private"should be removed.Secondly,need to correct the space error in the sentence，example "SRR5907429 ".'ascp -v -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh -k 1 -T -l200m anonftp#ftp.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR590/SRR5907429/SRR5907429.sra ~/sra_download'is the correct answer we need.enter image description here
Your problem:
the ascp syntax is:
Usage: ascp [OPTION] SRC... DEST
SRC to DEST, or multiple SRC to DEST dir
SRC, DEST format: [[user#]host:]PATH
Display full usage: -h,--help
You get this by simply executing ascp, get more with "ascp -h" and have a manual for it as well, or https://download.asperasoft.com/download/docs/entsrv/3.9.1/es_admin_linux/webhelp/index.html#dita/ascp_2.html
it is pretty much like "scp", but works also in "pull" mode.
so, you have:
options then one or multiple sources, then a single destination (always the last argument).
if the destination is: user#server:folder, then you do a push
if source is user#server:folder, then you do a pull
globally, you can only do a push or a pull at the same time. but there can be multiple sources, and always a single destination (on command line).
in you case you have:
options: -v -i ~/.aspera/connect/etc/asperaweb_id_dsa.openssh -k 1 -T -l200m
sources: anonftp#ftp-private.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR590/SRR5907429 /SRR5907429 .sra
destination:~/sra_download
the first source is: anonftp#ftp-private.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR590/SRR5907429
the other sources are: /SRR5907429 .sra
so you specify one remote source, two local sources, and one local destination.
This is the error you get.
My advice:
do not use the legacy syntax, as you did, but instead, use the advanced syntax:
ascp [options] --mode=<send|recv> --user=<user> --host=<server> sources... destination
There are plenty of options, for instance, if all your source files are in the same folder, you can use: --source-prefix=
you can also use file list file (i.e. a file that contains the list of files you want to transfer, in case it is long and generated by a script) or even file par list file.
Note also, that there is an interesting front end for aspera command line transfers:
https://www.rubydoc.info/gems/asperalm
In my configure.ac file, I have this:
AC_CONFIG_FILES([Makefile foo/bar.h],
[mkdir -p ../dir1 && cp foo/bar.h ../dir1]
)
The goal is to:
Generate the Makefile from Makefile.in
Generate foo/bar.h from foo/bar.h.in
Copy foo/bar.h to dir1/bar.h.
While it works, I'm pretty sure I've done that last part wrong. Looking at the generated output, I see:
case $ac_file$ac_mode in
"Makefile":F) mkdir -p ../dir1 && cp foo/bar.h ../dir1
;;
"foo/bar.h":F) mkdir -p ../dir1 && cp foo/bar.h ../dir1
;;
esac
So it looks like it is doing my 'mkdir' command once for each file in the file list which is a bit redundant. The fact that it does this in a 'case' statement suggests there is some way to specify commands to run specific to each file (otherwise why have a 'case'?).
What's the trick?
In case you don't need to keep bar.h in the dir foo, I suppose you can do
AC_CONFIG_FILES([Makefile bar.h:foo/bar.h.in])
source: https://www.gnu.org/software/autoconf/manual/autoconf-2.69/html_node/Configuration-Files.html#Configuration-Files
In case bar.h needs to be in both locations and a link is acceptable, use
AC_CONFIG_FILES([Makefile foo/bar.h])
AC_CONFIG_LINKS([bar.h:foo.bar.h])
source: https://www.gnu.org/software/autoconf/manual/autoconf-2.69/html_node/Configuration-Links.html#Configuration-Links
So it turns out I was misinterpreting what I was seeing.
Seeing that 'case' statement made me think there was some way to specify that some of the cmds applied to specific entries from the files parameter (something like [makefile:stuff1 foo/bar.h:stuff2]). But (thankfully) that's not why the 'case' is there.
The trick here is that at the point where the case statement is produced, we aren't just walking the entries from AC_CONFIG_FILES files. So in order to limit the cmds to the just AC_CONFIG_FILES entries, it uses a 'case.'
While my early attempts suggested that using two AC_CONFIG_FILES was not supported, that was wrong too.
My solution was to use 2 AC_CONFIG_FILES.
I feel like I must be doing something silly wrong, but I just can't get this to work. This is the command I am running from cmd:
inkscape.com "C:\path\ship.svg" -e --export-png="C:\Path\ship.png" --without-gui
In return, I get:
WARNING: File path "--export-png=C:\path\ship.png" includes directory that doesn't exist.
It does exist. What am I missing?
You should have used either -e or --export-png, not both, since they mean the same thing.
But According to the docs, -e and --export-png are no longer available. You should use -o or --export-filename=FILENAME instead. And still, you can use only one of them since -o is just the shortcut for --export-filename.
inkscape "C:\path\ship.svg" -o "C:\path\ship.png"
or
inkscape "C:\path\ship.svg" --export-filename="C:\path\ship.png"
Just an update for 2021 (it should be typed in oneline - broken down for readability only)
inkscape
--export-width=128
--export-type=png
--export-filename="C:\path\ship.png" "C:\path\build.svg"
or if you want transparent PNGs, add --export-background-opacity=0 to invocation arguments:
inkscape
--export-background-opacity=0
--export-width=128
--export-type=png
--export-filename="C:\path\ship.png" "C:\path\build.svg"
In inkscape version 1.0.2 following command will work:
inkscape --export-type="png" myfile.svg --export-filename=myfile.png
I need to find out which library will be loaded given in the information returned from /sbin/ldconfig. I came up with the following:
#!/bin/bash
echo $(dirname $(/sbin/ldconfig -p | awk "/$1/ {print \$4}" | head -n 1))
Running this results with:
$ whichlib libGL.so
/usr/X11R6/lib
This a two part question:
Will this produce a reliable result across platform?
Is there a slicker way to parse the output of ldconfig?
Thanks,
Paul
There're several ways the library is loaded by executeable:
1.
Using $LD_LIBRARY_PATH
Using ld cache
Libary with full path compiled into binary (-rpath gcc flag)
You're using option 2, while option 1 and 3 are not considered.
Depending on what exactly you're doing you may want to run ldd directly on the executable you're planning to run rather than the general case ldconfig.
Since you asked, you could write your script like this:
dirname "$(/sbin/ldconfig -p | awk "\$1 == "$1" {print \$4; exit}")"
It's a little more precise and has one less pipe. Also echo $(cmd) is redundant; you can just write cmd.