Here Document Output Redirection – How to Redirect

here-documentio-redirectionshell

How to redirect the output of below command in shell into logfile.

sqlplus -s "/nolog" <<EOF
conn / as sysdba
@?/sqlpatch/19282021/postinstall.sql
exit;
EOF

Just use redirection operator > at the first line:

sqlplus -s "/nolog" <<EOF >logfile
conn / as sysdba
@?/sqlpatch/19282021/postinstall.sql
exit;
EOF

You can also write >logfile at the beginning of the line, what is equally legal syntax in most shells, but less commonly practiced.

>logfile sqlplus -s "/nolog" <<EOF
conn / as sysdba
@?/sqlpatch/19282021/postinstall.sql
exit;
EOF

There are multiple ways to do this. The simplest is probably this:

cat <<EOF | sh
touch somefile
echo foo > somefile
EOF

Another, which is nicer syntax in my opinion:

(
cat <<EOF
touch somefile
echo foo > somefile
EOF
) | sh

This works as well, but without the subshell:

{
cat <<EOF
touch somefile
echo foo > somefile
EOF
} | sh

More variations:

cat <<EOF |
touch somefile
echo foo > somefile
EOF
  sh

Or:

{ cat | sh; } << EOF
touch somefile
echo foo > somefile
EOF

By the way, I expect the use of cat in your question is a placeholder for something else. If not, take it out, like this:

sh <<EOF
touch somefile
echo foo > somefile
EOF

Which could be simplified to this:

sh -c 'touch somefile; echo foo > somefile'

or:

sh -c 'touch somefile
echo foo > somefile'

Redirecting output instead of piping

sh >out <<EOF
touch somefile
echo foo > somefile
EOF

Using cat to get the equivalent of echo test > out:

cat >out <<EOF
test
EOF

Multiple Here Documents

( cat; echo ---; cat <&3 ) <<EOF 3<<EOF2
hi
EOF
there
EOF2

This produces the output:

hi
---
there

Here's what's going on:

The shell sees the ( ... ) and runs the enclosed commands in a subshell.
The cat and echo are simple enough. The cat <&3 says to run cat with file descriptor (fd) 0 (stdin) redirected from fd 3; in other words, cat out the input from fd 3.
Before the (...) is started, the shell sees the two here document redirects and substitutes fd 0 (<<EOF) and fd 3 (3<<EOF2) with the read-side of pipes
Once the initial command is started, the shell reads its stdin until EOF is reached and sends that to the write-side of the first pipe
Next, it does the same with EOF2 and the write-side of the second pipe

To make the hmmscan program write to stdout instead of a regular file, specify /dev/stdout instead of the regular filename. e.g.

$ hmmscan --domtblout /dev/stdout Pfam-A.hmm query.fasta