My goal is to use bcftools to check that the reference alleles in my dataset (vcf file) match with a reference genome (fasta file) using the fixref plugin.
Working on command line, I first set the following environment:
export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins
The following code is recommended for test datasets with mismatches:
bcftools +fixref test.bcf -Ob -o output.bcf -- -f ref.fa -m top
When I run this code using my own files (please note that my data is .vcf, not .bcf) I get the following error:
[main] Unrecognized command
If I simply enter:
bcftools
I get a list of the only 5 commands (view, index, cat, ld, ldpair) that I can use. So although I've set the environment, does it somehow need to be activated? Do I need to run my command through a bash script?
bcftools
was pointing to a deprecated version of bcftools (0.1.19) in ../bin/, while
BCFTOOLS_PLUGINS=/path/to/bcftools/plugins
was pointing to the plugins for bcftools version 1.10.2 outside /bin/
Replacing ../bin/bcftools (0.1.19 with 1.10.2) was the fix.
I have followed the GitHub to setup. I have installed pip, MariaDB, bench, Redis.
After I run the command bench init frappe-bench and cd frappe-bench I don't allow me to create a new site. The following is an error that IO encountered.
/usr/local/Cellar/python/3.7.5/bin/python3.7: Error while finding module specification for 'frappe.utils.bench_helper' (ModuleNotFoundError: No module named 'frappe')
Usage: bench [OPTIONS] COMMAND [ARGS]...
Try "bench --help" for help.
Error: No such command "new-site".
I have also changed in my.conf to
[mysqld]
innodb-file-format=barracuda
innodb-file-per-table=1
innodb-large-prefix=1
character-set-client-handshake = FALSE
character-set-server = utf8mb4
collation-server = utf8mb4_unicode_ci
[mysql]
default-character-set = utf8mb4
After bench init frappe-bench
cd env
source env/bin/activate
pip install -e ./apps/frappe --no-cache-dir
bench build
Reference: https://discuss.erpnext.com/t/mac-os-setup-failed/53422/3
I am trying to install a mongo client via chef. Essentially this is what I have been doing in manual installs:
sudo vi /etc/yum.repos.d/mongodb.repo
[mongodb]
name=MongoDB Repository
baseurl=http://downloads-distro.mongodb.org/repo/redhat/os/x86_64/
gpgcheck=0
enabled=1
sudo yum install mongodb-org-shell-2.6.7
I don't want to reinvent the wheel here, nor do I want to install anything other than the shell. This cookbook looks like a good resource, but I cannot get it to install just the shell:
https://github.com/edelight/chef-mongodb
But it seems to not allow for any of the main components to be installed. Will i need to LWRP?
Well i picked apart the mongodb cookbook - to this tune:
yum_repository 'mongodb-org-3.0' do
description 'mongodb RPM Repository'
baseurl "http://repo.mongodb.org/yum/redhat/$releasever/mongodb-org/3.0/#{node['kernel']['machine'] =~ /x86_64/ ? 'x86_64' : 'i686'}"
action :create
gpgcheck false
enabled true
end
case node['platform_family']
when 'debian'
# this options lets us bypass complaint of pre-existing init file
# necessary until upstream fixes ENABLE_MONGOD/DB flag
packager_opts = '-o Dpkg::Options::="--force-confold" --force-yes'
when 'rhel'
# Add --nogpgcheck option when package is signed
# see: https://jira.mongodb.org/browse/SERVER-8770
packager_opts = '--nogpgcheck'
else
packager_opts = ''
end
package node[:frt_mongodb][:package_name] do
options packager_opts
action :install
version node[:frt_mongodb][:package_version]
end
That said it looks like I should be able to use that cookbook configured with the right attributes to aCcomplish this. The biggest problem is that the recipe within manipulates files that aren't necessary for the shell.
I have doxygen 1.8.5 and Doxverilog (for doxygen 1.7.0). Following the instructions quoted below I get messages saying that patches have previously been applied. Then some of the HUNKs fail.
If I proceed anyway and set up the verilog.cfg, running doxygen with this cfg produces
"Warning: ignoring unsupported tag `OPTIMIZE_OUTPUT_VERILOG =' at line 35, file verilog.cfg"
Then blank output.
The instructions I'm using to setup doxverilog are:
install the doxygen-1.7.0 sources
1. copy the Verilog files verilogparser.y verlogscanner.l and the source files to the doxygen-1.7.0\src directory
2. copy the patch file verilog.patch to directory doxygen-1.7.0
3. open a shell in the doxygen-1.7.0 directory
3.1 configure doxygen
sh configure
3.2 make patch # patch -p1 < verilog.patch
4 compile the source files
make all
5 If the compilation was successful create a doxygen configuration file with # doxygen -s -g verilog.cfg
In the configuration file you should see the option OPTIMIZE_OUTPUT_VERILOG.
The file patterns for the Verilog parser are *.v and *.V
I want to run GNU Screen from within an Emacs term-mode buffer. When I try to do this I get an error:
$ screen
Cannot find terminfo entry for 'eterm-color'.
This error suggests that I should install the eterm-color terminfo entry. I attempted to do this in 2 ways which both failed.
The first attempt was to use the TERMINFO environment variable.
My .bashrc:
export TERMINFO=~/.terminfo
Then I did:
$ mkdir -p ~/.terminfo/e/
$ cp /usr/local/Cellar/emacs/23.3a/share/emacs/23.3/etc/e/* ~/.terminfo/e/
In the term-mode buffer the eterm-color entry is not found. It says that it gets eterm-color from TERMCAP instead of from the actual file.
$ infocmp
# Reconstructed via infocmp from file: TERMCAP
eterm-color,
am, mir, xenl,
colors#8, cols#138, it#8, lines#41, pairs#64,
bel=^G, bold=\E[1m, clear=\E[H\E[J, cr=^M,
csr=\E[%i%p1%d;%p2%dr, cub=\E[%p1%dD, cub1=^H,
cud=\E[%p1%dB, cud1=^J, cuf=\E[%p1%dC, cuf1=\E[C,
cup=\E[%i%p1%d;%p2%dH, cuu=\E[%p1%dA, cuu1=\E[A,
dch=\E[%p1%dP, dch1=\E[P, dl=\E[%p1%dM, dl1=\E[M, ed=\E[J,
el=\E[K, el1=\E[1K, home=\E[H, ht=^I, ich=\E[%p1%d#,
il=\E[%p1%dL, il1=\E[L, ind=^J, invis=\E[8m, kbs=\177,
kcub1=\EOD, kcud1=\EOB, kcuf1=\EOC, kcuu1=\EOA,
kdch1=\E[3~, kend=\E[4~, khome=\E[1~, knp=\E[6~, kpp=\E[5~,
nel=^M^J, op=\E[39;49m, rc=\E8, rev=\E[7m, rmir=\E[4l,
rmso=\E[27m, rmul=\E24m, rs1=\Ec, sc=\E7, setab=\E[4%p1%dm,
setaf=\E[3%p1%dm, sgr0=\E[m, smir=\E[4h, smso=\E[7m,
smul=\E[4m,
The second attempt was to use symlinks.
$ sudo mkdir /usr/share/terminfo/e/
$ sudo cp /usr/local/Cellar/emacs/23.3a/share/emacs/23.3/etc/e/* /usr/share/terminfo/e/
This failed in the same way as the first attempt.
Why did neither attempt work? How do I get the eterm-color terminfo entry installed?
I am running OS X 10.6.8 and Emacs 23.3.1.
The following worked for me on FreeBSD.
Put the termcap entry pasted below in /usr/share/misc/termcap and run # cd /usr/share/misc/ && cap_mkdb termcap.
# Termcap entry for eterm-color (taken from $TERMCAP set by emacs and formatted)
eterm-color|Emacs term.el terminal emulator term-protocol-version 0.96:\
:am:bs:mi:pt:xn:\
:Co#8:co#166:li#48:pa#64:\
:#7=\E[4~:AB=\E[4%dm:AF=\E[3%dm:AL=\E[%dL:DC=\E[%dP:\
:DL=\E[%dM:DO=\E[%dB:IC=\E[%d#:LE=\E[%dD:RI=\E[%dC:\
:UP=\E[%dA:al=\E[L:bl=^G:cb=\E[1K:cd=\E[J:ce=\E[K:\
:cl=\E[H\E[J:cm=\E[%i%d;%dH:cr=^M:cs=\E[%i%d;%dr:dc=\E[P:\
:dl=\E[M:do=^J:ei=\E[4l:ho=\E[H:im=\E[4h:kD=^[[3~:\
:kN=\E[6~:kP=\E[5~:kb=^?:kd=\EOB:kh=\E[1~:kl=\EOD:\
:kr=\EOC:ku=\EOA:le=^H:md=\E[1m:me=\E[m:mk=\E[8m:mr=\E[7m:\
:nd=\E[C:op=\E[39;49m:r1=\Ec:rc=\E8:sc=\E7:se=\E[27m:sf=^J:\
:so=\E[7m:ta=^I:ue=\E[m:\
:up=\E[A:us=\E[4m: