While lmod support fish from version 7.4 onwards, I have to use servers with an older version. How can I make it work with fish? (Even if in limited capacity.)
This solution let me run commands like module load R. It may fail in the general case.
Define a convenience function as follows:
function module
eval $LMOD_CMD bash $argv | lmod_bash_to_fish.py | source -
end
where lmod_bash_to_fish.py has the contents:
#!/usr/bin/env python3
import re
import sys
f = sys.stdin
while True:
line = f.readline()
if not line:
break
match = re.match(r'^(\w+)="(.+)";\n$', line)
if not match:
raise RuntimeError("Unexpected line: {}".format(line))
var, val = match.groups()
line = f.readline()
if line != "export {};\n".format(var):
raise RuntimeError("Variable not immediately exported: {}".format(line))
if var == 'PATH':
val = " ".join('"{}"'.format(elem) for elem in val.split(':'))
print("set -gx fish_user_paths {}".format(val))
continue
print("set -gx {} \"{}\"".format(var, val))
Related
I am getting a java.nio.file.ProviderMismatchException when I run the following script:
process a {
output:
file _biosample_id optional true into biosample_id
script:
"""
touch _biosample_id
"""
}
process b {
input:
file _biosample_id from biosample_id.ifEmpty{file("_biosample_id")}
script:
def biosample_id_option = _biosample_id.isEmpty() ? '' : "--biosample_id \$(cat _biosample_id)"
"""
echo \$(cat ${_biosample_id})
"""
}
i'm using a slightly modified version of Optional Input pattern.
Any ideas on why I'm getting the java.nio.file.ProviderMismatchException?
In your script block, _biosample_id is actually an instance of the nextflow.processor.TaskPath class. So to check if the file (or directory) is empty you can just call it's .empty() method. For example:
script:
def biosample_id_option = _biosample_id.empty() ? '' : "--biosample_id \$(< _biosample_id)"
I like your solution - I think it's neat. And I think it should be robust (but I haven't tested it). The optional input pattern that is recommended will fail when attempting to stage missing input files to a remote filesystem/object store. There is a solution however, which is to keep an empty file in your $baseDir and point to it in your scripts. For example:
params.inputs = 'prots/*{1,2,3}.fa'
params.filter = "${baseDir}/assets/null/NO_FILE"
prots_ch = Channel.fromPath(params.inputs)
opt_file = file(params.filter)
process foo {
input:
file seq from prots_ch
file opt from opt_file
script:
def filter = opt.name != 'NO_FILE' ? "--filter $opt" : ''
"""
your_commad --input $seq $filter
"""
}
I have got errors like .command.sh: line 2: syntax error near unexpected token `('
/*
* Step 3
*/
chr_length = file(params.chr_length)
process create_bedgraph_and_bigwig {
publishDir "${params.outdir}/bedgraphandbigwig", mode: 'copy'
input:
set val(sample_id), file(vector_log) from vector_log_ch
set val(sample_id), file(target_query_bam) from target_query_bam_ch
file chr_length
output:
set val(sample_id), file("${sample_id}.bedgraph.log.txt") into bed_log_ch
set val(sample_id), file("${sample_id}.bed") into bed_ch
set val(sample_id), file("${sample_id}.clean.bed") into clean_bed_ch
set val(sample_id), file("${sample_id}.fragments.bed") into fragments_bed_ch
set val(sample_id), file("${sample_id}.sorted.fragments.bed") into sorted_fragments_bed_ch
shell:
'''
def fp = file(${vector_log})
def lines = fp.readLines()
def line3 = lines[3].split(' ')[4].toInteger()
def line4 = lines[4].split(' ')[4].toInteger()
def aln_sum = (10000/(line3 + line4)).toString()
bedtools bamtobed -bedpe -i !{target_query_bam} > !{sample_id}.bed 2>!{sample_id}.bedgraph.log.txt
awk '$1==$4 && $6-$2 < 1000 {{print $0}}' !{sample_id}.bed > !{sample_id}.clean.bed 2>!{sample_id}.bedgraph.log.txt
cut -f 1,2,6 !{sample_id}.clean.bed > !{sample_id}.fragments.bed 2>!{sample_id}.bedgraph.log.txt
sort -k 1,1 !{sample_id}.fragments.bed > !{sample_id}.sorted.fragments.bed
'''
}
The simple answer is to avoid using 'def' if the variable needs to be used in a shell definition or template. I couldn't actually find this after a quick search of the documentation, but I did find this note from the author:
Using groovy native string interpolation that would work, but when using the !{..} syntax scripts variable cannot be declared locally using the def keyword.
To summarise:
script/shell variable should be defensively declared in the local scope using the def keyboard
do not use def when:
i. the variable needs to be referenced as a output value
ii. the variable needs to be used in a shell template
https://github.com/nextflow-io/nextflow/issues/678#issuecomment-386206123
I tried to program an app in tkinter that would load random lines from a file you select from a pull down menu and display the selected line in a text window.
It seems like the variable "var" in insert_text does not return the selected "option" but rather an "empty" string resulting in a the following error:
"File not found error" (FileNotFoundError: [Errno2] No such file or
directory: '').
Please help!
#!/usr/bin/env python
# Python 3
import tkinter
from tkinter import ttk
import random
class Application:
def __init__(self, root):
self.root = root
self.root.title('Random Stuff')
ttk.Frame(self.root, width=450, height=185).pack()
self.init_widgets()
var = tkinter.StringVar(root)
script = var.get()
choices = ['option1', 'option2', 'option3']
option = tkinter.OptionMenu(root, var, *choices)
option.pack(side='right', padx=10, pady=10)
def init_widgets(self):
ttk.Button(self.root, command=self.insert_txt, text='Button', width='10').place(x=10, y=10)
self.txt = tkinter.Text(self.root, width='45', height='5')
self.txt.place(x=10, y=50)
def insert_txt(self):
var = tkinter.StringVar(root)
name = var.get()
line = random.choice(open(str(name)).readlines())
self.txt.insert(tkinter.INSERT, line)
if __name__ == '__main__':
root = tkinter.Tk()
Application(root)
root.mainloop()
That's because you're just creating an empty StringVar that isn't modified later, thus returning an empty string.
The OptionMenu takes the command parameter that calls the specified method every time another option is selected. Now, you can call a method like this, replacing you insert_txt:
def __init__(self):
# ...
self.var = tkinter.StringVar()
self.options = tkinter.OptionMenu(root, var, *choices, command=self.option_selected)
# ...
def option_selected(self, event):
name = self.var.get()
# The stuff you already had
Additionally, you have to empty the Text widget, otherwise the previous text would stay. I think the Entry widget is better for that, too.
I want to see all of the unique IDs that are specific for a virtual machine such as:
hardware ID, CPU ID, UUID , Mac address and etc.
could anybody please help me to find these IDs??
I can help you finding some of these. For rest of the things you have to search the doc.
Install pyVmomi and run the following code.
EDIT: Changed the code to run on esx host. Simply run it by python .py
Now to know how this code is working. You have to learn Manged Objects. For example here we are working with the Manged Object vm and this object has many properties listed in the doc. So to retrieve uuid of a vm we are invoking vm.config.uuid. Regarding other details you have to go through the VirtualMachine object see what all properties you nedd.
import sys
import atexit
import time
from pyVmomi import vim, vmodl
from pyVim.connect import Disconnect
from pyVim import connect
inputs = {'esx_ip': '15.22.10.10',
'esx_password': 'Password123',
'esx_user': 'root',
'vm_name': 'ubuntu',
}
def wait_for_task(task, actionName='job', hideResult=False):
"""
Waits and provides updates on a vSphere task
"""
while task.info.state == vim.TaskInfo.State.running:
time.sleep(2)
if task.info.state == vim.TaskInfo.State.success:
if task.info.result is not None and not hideResult:
out = '%s completed successfully, result: %s' % (actionName, task.info.result)
print out
else:
out = '%s completed successfully.' % actionName
print out
else:
out = '%s did not complete successfully: %s' % (actionName, task.info.error)
raise task.info.error
print out
return task.info.result
def get_obj(content, vimtype, name):
"""
Get the vsphere object associated with a given text name
"""
obj = None
container = content.viewManager.CreateContainerView(content.rootFolder, vimtype, True)
for c in container.view:
if c.name == name:
obj = c
break
return obj
def main():
si = None
try:
print "Trying to connect ..."
si = connect.Connect(inputs['vcenter_ip'], 443, inputs['vcenter_user'], inputs['vcenter_password'])
except IOError, e:
pass
if not si:
print "Cannot connect to specified host using specified username and password"
sys.exit()
print "Connected to vcenter!"
atexit.register(Disconnect, si)
content = si.RetrieveContent()
# Get the VirtualMachine Object
vm = get_obj(content, [vim.VirtualMachine], inputs['vm_name'])
print "GuestID: ", vm.config.guestId
print "UUID: ", vm.config.uuid
print "Version: ", vm.config.version
for device in vm.config.hardware.device:
if isinstance(device, vim.vm.device.VirtualEthernetCard):
print "MAC Address: ", device.macAddress
#Example of changing UUID:
new_uuid = '423ffff0-5d62-d040-248c-4538ae2c734f'
vmconf = vim.vm.ConfigSpec()
vmconf.uuid = new_uuid
task = vm.ReconfigVM_Task(vmconf)
wait_for_task(task, si)
print "Successfully changed UUID"
print "New UUID: ", vm.config.uuid
if __name__ == "__main__":
main()
is it possible to use redis's MOVE command to move all keys from 1 database to another? The move command only moves 1 key, but I need to move all the keys in the database.
I would recommend taking a look at the following alpha version app to backup and restore redis databases.. (you can install it via gem install redis-dump). You could redis-dump your databaseand then redis-load into another database via the --database argument.
redis-dump project
If this doesn't fit your purposes, you may need to make use of a scripting language's redis bindings (or alternatively throw something together using bash / redis-cli / xargs, etc). If you need assistance along these lines then we probably need more details first.
I've wrote a small python script to move data between two redis servers:(only support list and string types, and you must install python redis client):
'''
Created on 2011-11-9
#author: wuyi
'''
import redis
from optparse import OptionParser
import time
def mv_str(r_source, r_dest, quiet):
keys = r_source.keys("*")
for k in keys:
if r_dest.keys(k):
print "skipping %s"%k
continue
else:
print "copying %s"%k
r_dest.set(k, r_source.get(k))
def mv_list(r_source, r_dest, quiet):
keys = r_source.keys("*")
for k in keys:
length = r_source.llen(k)
i = 0
while (i<length):
print "add queue no.:%d"%i
v = r_source.lindex(k, i)
r_dest.rpush(k, v)
i += 1
if __name__ == "__main__":
usage = """usage: %prog [options] source dest"""
parser = OptionParser(usage=usage)
parser.add_option("-q", "--quiet", dest="quiet",
default = False, action="store_true",
help="quiet mode")
parser.add_option("-p", "--port", dest="port",
default = 6380,
help="port for both source and dest")
parser.add_option("", "--dbs", dest="dbs",
default = "0",
help="db list: 0 1 120 220...")
parser.add_option("-t", "--type", dest="type",
default = "normal",
help="available types: normal, lpoplist")
parser.add_option("", "--tmpdb", dest="tmpdb",
default = 0,
help="tmp db number to store tmp data")
(options, args) = parser.parse_args()
if not len(args) == 2:
print usage
exit(1)
source = args[0]
dest = args[1]
if source == dest:
print "dest must not be the same as source!"
exit(2)
dbs = options.dbs.split(' ')
for db in dbs:
r_source = redis.Redis(host=source, db=db, password="", port=int(options.port))
r_dest = redis.Redis(host=dest, db=db, password="", port=int(options.port))
print "______________db____________:%s"%db
time.sleep(2)
if options.type == "normal":
mv_str(r_source, r_dest, options.quiet)
elif options.type == "lpoplist":
mv_list(r_source, r_dest, options.quiet)
del r_source
del r_dest
you can try my own tool, rdd
it's a command line utility,
can dump database to a file, work on it (filter, match, merge, ...), and back it in a redis instance
take care, alpha stage, https://github.com/r043v/rdd/
Now that redis has scripting using lua, you can easily write a command that loops through all the keys, checks their type and moves them accordingly to a new database.
I suggest you can try it as below:
1. copy the rdb file to another dir;
2. modify the rdb file name;
3. modify the redis configure file adapter to the new db;