On Tue, 13 Aug 2019 at 05:04, Lee wrote:
> On 8/12/19, Greg Wooledge wrote:
> > On Mon, Aug 12, 2019 at 01:56:46PM -0400, Lee wrote:
>> What's the difference between ${d} and "${d}"? Or is that a bashism
>> also? (all my scripts use /bin/sh so I'm pretty clueless wrt bash)
> >
> > For more deta
On 8/12/19, Greg Wooledge wrote:
> On Mon, Aug 12, 2019 at 01:56:46PM -0400, Lee wrote:
>> What's the difference between ${d} and "${d}"? Or is that a bashism
>> also? (all my scripts use /bin/sh so I'm pretty clueless wrt bash)
>
> This applies to both sh and bash.
>
> An unquoted substitution,
On Mon, Aug 12, 2019 at 01:56:46PM -0400, Lee wrote:
> What's the difference between ${d} and "${d}"? Or is that a bashism
> also? (all my scripts use /bin/sh so I'm pretty clueless wrt bash)
This applies to both sh and bash.
An unquoted substitution, like $d or ${d}, undergoes several steps. T
On 8/12/19, Greg Wooledge wrote:
> On Mon, Aug 12, 2019 at 01:37:16PM -0400, Lee wrote:
>> On 8/12/19, Greg Wooledge wrote:
>> > On Mon, Aug 12, 2019 at 01:19:45PM -0400, Lee wrote:
>> >> On 8/12/19, Greg Wooledge wrote:
>> >> > P.S. it would also have been possible to work around the carriage
>
On Mon, Aug 12, 2019 at 01:37:16PM -0400, Lee wrote:
> On 8/12/19, Greg Wooledge wrote:
> > On Mon, Aug 12, 2019 at 01:19:45PM -0400, Lee wrote:
> >> On 8/12/19, Greg Wooledge wrote:
> >> > P.S. it would also have been possible to work around the carriage
> >> > return
> >> > issues with IFS, but
On 8/12/19, Greg Wooledge wrote:
> On Mon, Aug 12, 2019 at 01:19:45PM -0400, Lee wrote:
>> On 8/12/19, Greg Wooledge wrote:
>> > P.S. it would also have been possible to work around the carriage
>> > return
>> > issues with IFS, but your dos2unix approach is perfectly valid as well.
>>
>> Just ou
On Mon, Aug 12, 2019 at 01:19:45PM -0400, Lee wrote:
> On 8/12/19, Greg Wooledge wrote:
> > P.S. it would also have been possible to work around the carriage return
> > issues with IFS, but your dos2unix approach is perfectly valid as well.
>
> Just out of curiosity - how?
while IFS=$' \t\r\n' r
On 8/12/19, Greg Wooledge wrote:
> On Sun, Aug 11, 2019 at 02:10:06PM -0400, Stephen P. Molnar wrote:
>> Thanks to all that shared their expertise.
>>
>> #!/bin/bash
>> while IFS= read -r d
>> do
>> cd "${d}_apo-3k9b"
>> echo "${d}_apo-3k9b"
>> echo "${d}_apo-3k9b.dpf"
>> /home/com
On 08/12/2019 09:39 AM, Greg Wooledge wrote:
On Sun, Aug 11, 2019 at 02:10:06PM -0400, Stephen P. Molnar wrote:
Thanks to all that shared their expertise.
#!/bin/bash
while IFS= read -r d
do
cd "${d}_apo-3k9b"
echo "${d}_apo-3k9b"
echo "${d}_apo-3k9b.dpf"
/home/comp/Apps/
On Sun, Aug 11, 2019 at 02:10:06PM -0400, Stephen P. Molnar wrote:
> Thanks to all that shared their expertise.
>
> #!/bin/bash
> while IFS= read -r d
> do
> cd "${d}_apo-3k9b"
> echo "${d}_apo-3k9b"
> echo "${d}_apo-3k9b.dpf"
> /home/comp/Apps/Autodock/autodock4 -p "${d}_apo-3k9b.
On 08/11/2019 11:56 AM, Lee wrote:
On 8/11/19, David wrote:
On Mon, 12 Aug 2019 at 01:07, Stephen P. Molnar
wrote:
Thanks for the suggestion.
However,
comp@AbNormal:~/Apps/Models/1-PhosphorusLigands/Acetylcholinesterases/3K9B/Results$
./Run.ligand.list.sh
./Run.ligand.list.sh: line 4: c
On 8/11/19, David wrote:
> On Mon, 12 Aug 2019 at 01:07, Stephen P. Molnar
> wrote:
>>
>> Thanks for the suggestion.
>> However,
>> comp@AbNormal:~/Apps/Models/1-PhosphorusLigands/Acetylcholinesterases/3K9B/Results$
>> ./Run.ligand.list.sh
>> ./Run.ligand.list.sh: line 4: cd: $'Acetylcholine\r_ap
On Mon, 12 Aug 2019 at 01:07, Stephen P. Molnar wrote:
>
> Thanks for the suggestion.
> However,
> comp@AbNormal:~/Apps/Models/1-PhosphorusLigands/Acetylcholinesterases/3K9B/Results$
> ./Run.ligand.list.sh
> ./Run.ligand.list.sh: line 4: cd: $'Acetylcholine\r_apo-3k9b': No such
> file or directory
On 08/11/2019 10:39 AM, David wrote:
On Sun, 11 Aug 2019 at 23:18, Stephen P. Molnar wrote:
I am running an up-to-date installation of Buster on my Linux platform
and have run into a strange problem with a bash script.
[...]
for d in $(cat ligand.list)
This line is the problem, it is vul
On Sun, 11 Aug 2019 at 23:18, Stephen P. Molnar wrote:
>
> I am running an up-to-date installation of Buster on my Linux platform
> and have run into a strange problem with a bash script.
[...]
> for d in $(cat ligand.list)
This line is the problem, it is vulnerable to various kinds
of breakage
On Sun, Aug 11, 2019 at 09:17:53AM -0400, Stephen P. Molnar wrote:
> I am running an up-to-date installation of Buster on my Linux
> platform and have run into a strange problem with a bash script.
>
> I have a number of ligand protein docking applications which involve
> ligand sets docking on a
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